Changeset 1200

Timestamp:

Mar 20, 2026, 4:42:36 PM (21 hours ago)

Author:

sommeria

Message:

bug repaired for civ image rescale

Location:

trunk/src

Files:

• mouse_motion.m (modified) (1 diff)
• mouse_up.m (modified) (4 diffs)
• plot_field.m (modified) (19 diffs)
• series.m (modified) (41 diffs)
• series.xml.default (modified) (1 diff)
• series/civ_input.fig (modified) (previous)
• series/civ_input.m (modified) (1 diff)
• series/civ_series.m (modified) (12 diffs)
• uvmat.fig (modified) (previous)
• uvmat.m (modified) (22 diffs)

trunk/src/mouse_motion.m

@@ -37 +37 @@
 end
 hhCurrentFig=guidata(hCurrentFig);%handles of the elements in the GUI containing the current figure (uvmat or view_field)
+if isempty(hhCurrentFig)
+    return
+end
 CheckZoom=get(hhCurrentFig.CheckZoom,'Value');% check for zoom on mode
 CheckZoomFig=get(hhCurrentFig.CheckZoomFig,'Value');% check for zoom sub fig creation mode

trunk/src/mouse_up.m

@@ -151 +151 @@
                     else
                         hhview_field=guidata(hview_field);
-                        [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%update an existing  plot in view_field
+                        [~,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%update an existing  plot in view_field
                         errormsg=fill_GUI(PlotParam,hview_field);
                     end
@@ -168 +168 @@
                 else
                     UvData.PlotAxes=ProjData;
-                    [PlotType,PlotParam]=plot_field(ProjData,hhuvmat.PlotAxes,read_GUI(huvmat));%update an existing field plot
+                    [~,PlotParam]=plot_field(ProjData,hhuvmat.PlotAxes,read_GUI(huvmat));%update an existing field plot
                     errormsg=fill_GUI(PlotParam,huvmat);
                 end
@@ -201 +201 @@
 
 %% creation or update of a  zoom sub-plot
-if CheckZoomFig && isequal(get(hcurrentfig,'SelectionType'),'normal')&&...%if left button has been pressed
+CheckZoomFigActivate=CheckZoomFig && strcmp(get(hcurrentfig,'SelectionType'),'normal')&&...%if left button has been pressed
      ~isempty(CurrentOrigin) && ~isequal(CurrentOrigin(1),xy(1,1)) && ~isequal(CurrentOrigin(2),xy(1,2))%if mouse moved in x and y since presed down
+if CheckZoomFigActivate 
     hparentfig=hcurrentfig;
     %open or update a new zoom figure if a rectangle has been drawn
     if ishandle(hcurrentaxes)
         if isfield(AxeData,'CurrentRectZoom') && ~isempty(AxeData.CurrentRectZoom) && ishandle(AxeData.CurrentRectZoom)
-            %PosRect=get(AxeData.CurrentRectZoom,'Position');
             if isfield(AxeData,'CurrentVec') && ~isempty(AxeData.CurrentVec) && ishandle(AxeData.CurrentVec)
                 delete(AxeData.CurrentVec)
@@ -391 +391 @@
 %------------------------------------------------------------------------
 function close_fig(ggg,eventdata,hparent)
-
-hfig=get(get(hparent,'parent'),'parent');
-hbutton=findobj(hfig,'Tag','CheckZoomFig');
-if ~isempty(hbutton)
-    set(hbutton,'Value',0)% desactivate the zoom fig option
-end
-delete(hparent)  % delete the rectangle showing the zoom graph in the parent fig
-
+if isvalid(hparent)
+    figparent=get(hparent,'parent');
+    if ~isempty(figparent)
+        hfig=get(figparent,'parent');
+        hbutton=findobj(hfig,'Tag','CheckZoomFig');
+        if ~isempty(hbutton)
+            set(hbutton,'Value',0)% desactivate the zoom fig option
+        end
+        delete(hparent)  % delete the rectangle showing the zoom graph in the parent fig
+    end
+end

trunk/src/plot_field.m

@@ -178 +178 @@
 AxeData=get(haxes,'UserData');
 
-%% 2D plots 
-if isempty(index_2D)
-    plot_plane([],[],haxes,[]);%removes images or vector plots in the absence of 2D field plot
+%% 2D plots
+if isempty(index_2D) %removes images or vector plots in the absence of 2D field plot
+    hima=findobj(haxes,'Tag','ima');% search existing image in the current axes
+    if  ishandle(hima)
+        delete(hima)
+    end
+    hvec=findobj(haxes,'Tag','vel');% search existing vectors in the current axes
+    if ~isempty(hvec)
+        delete(hvec);
+    end
 else  %plot 2D field
-%     if ~exist('PosColorbar','var'),PosColorbar=[];end;
+    %     if ~exist('PosColorbar','var'),PosColorbar=[];end;
     [~,PlotParamOut,PlotType,errormsg]=plot_plane(Data,CellInfo(index_2D),haxes,PlotParamOut);
     AxeData.NbDim=2;
-    if testzoomaxes && isempty(errormsg)
-        [zoomaxes,PlotParamOut,~,errormsg]=plot_plane(Data,CellInfo(index_2D),zoomaxes,PlotParamOut);
+    if testzoomaxes && isempty(errormsg)% updater the plot on the attached axis
+        PlotParamZoom=PlotParamOut;
+        PlotParamZoom.Axes.CheckFixLimits=1;
+        XLim=get(zoomaxes,'XLim');
+        YLim=get(zoomaxes,'YLim');
+        PlotParamZoom.Axes.MinX=XLim(1);
+        PlotParamZoom.Axes.MaxX=XLim(2);
+        PlotParamZoom.Axes.MinY=YLim(1);
+        PlotParamZoom.Axes.MaxY=YLim(2);
+        PlotParamZoom.Axes.CheckZoomFig=0;
+        [zoomaxes,~,~,errormsg]=plot_plane(Data,CellInfo(index_2D),zoomaxes,PlotParamZoom);
         AxeData.ZoomAxes=zoomaxes;
     end
@@ -275 +291 @@
 % --- plot 0D fields: display data values without plot
 %------------------------------------------------------------------
-function errormsg=plot_text(FieldData,CellInfo,htext)
+function errormsg=plot_text(FieldData,CellInfo,~)
 
 errormsg='';
-txt_cell={};
-Data={};
 VarIndex=[];
-for icell=1:length(CellInfo)
-    
+for icell=1:length(CellInfo)    
     % select types of  variables to be projected
     ListProj={'VarIndex_scalar','VarIndex_image','VarIndex_color','VarIndex_vector_x','VarIndex_vector_y'};
@@ -617 +630 @@
         end
         Val=pdf2stat(x,pdf_val);
-        Column=mat2cell(Val,ones(13,1),ones(1,size(Val,2)));
+        Column=num2cell(Val,ones(13,1),ones(1,size(Val,2)));
         if size(Val,2)==1%single component
             TitleBar={VarName};
@@ -665 +678 @@
 test_ima=0; %default: test for image or map plot
 test_vec=0; %default: test for vector plots
-test_black=0;
 test_false=0;
 test_C=0;
@@ -681 +693 @@
     ivar_Y=CellInfo{icell}.CoordIndex(end-1); % defines (unique)index for the variable representing unstructured y coordinate (default =[])
     ivar_C=[];
-    if isfield(CellInfo{icell},'VarIndex_scalar')
-        ivar_C=[ivar_C CellInfo{icell}.VarIndex_scalar];
-    end
-    if isfield(CellInfo{icell},'VarIndex_image')
-        ivar_C=[ivar_C CellInfo{icell}.VarIndex_image];
-    end
-    if isfield(CellInfo{icell},'VarIndex_color')
-        ivar_C=[ivar_C CellInfo{icell}.VarIndex_color];
-    end
-    if isfield(CellInfo{icell},'VarIndex_ancillary')
-        ivar_C=[ivar_C CellInfo{icell}.VarIndex_ancillary];
-    end
-    if numel(ivar_C)>1
-        errormsg= 'error in plot_field: too many scalar inputs';
-        return
-    end
+    ListFields=fields(CellInfo{icell});
+    for ilist=1:numel(ListFields)
+        if ismember(ListFields{ilist},{'VarIndex_scalar','VarIndex_image','VarIndex_color','VarIndex_ancillary'})
+            ivar_C=CellInfo{icell}.(ListFields{ilist});
+            break % do not allow more than one scalar 
+        end
+    end 
     ivar_F=[];
     if isfield(CellInfo{icell},'VarIndex_warnflag')
@@ -734 +737 @@
             end
             if isfield(PlotParam.Vectors,'ColorScalar') && ~isempty(PlotParam.Vectors.ColorScalar)
-                [VarVal,ListVarName,VarAttribute,errormsg]=calc_field_interp([],Data,PlotParam.Vectors.ColorScalar);
+                [VarVal,~,~,errormsg]=calc_field_interp([],Data,PlotParam.Vectors.ColorScalar);
                 if ~isempty(VarVal)
                     vec_C=reshape(VarVal{1},1,numel(VarVal{1}));
@@ -745 +748 @@
                 if ~isempty(ivar_F)%~(isfield(PlotParam.Vectors,'HideWarning')&& isequal(PlotParam.Vectors.HideWarning,1))
                     vec_F=Data.(Data.ListVarName{ivar_F}); % warning flags for  dubious vectors
-                    vec_FF(find(vec_F==-2))=1;%set alseFlag to 1(edge of the search box)
+                    vec_FF(vec_F==-2)=1;%set FalseFlag to 1(edge of the search box)
                 end
             end
@@ -790 +793 @@
                 DCoord_y_min=min(DCoord_y);
                 DCoord_y_max=max(DCoord_y);
-                if sign(DCoord_y_min)~=sign(DCoord_y_max);% =1 for increasing values, 0 otherwise
+                if sign(DCoord_y_min)~=sign(DCoord_y_max)% =1 for increasing values, 0 otherwise
                     errormsg=['errror in plot_field.m: non monotonic dimension variable ' YName ];
                     return
@@ -877 +880 @@
     if isfield(PlotParam.Scalar,'CheckBW') && ~isempty(PlotParam.Scalar.CheckBW)
         ColorMap=PlotParam.Scalar.CheckBW;%PlotParam.Scalar.CheckBW is char string indicating the colormap type
-    elseif ((siz==2) && (isa(A,'uint8')|| isa(A,'uint16')))% non color images represented in gray scale by default
+    elseif siz==2 && (isa(A,'uint8')||isa(A,'uint16'))% non color images represented in gray scale by default
         ColorMap='grayscale';
     end
@@ -962 +965 @@
         % fill the space between contours if opacity is undefined or =1
         if isequal(Opacity,1)
-            [var,hcontour]=contour(haxes,x_cont,y_cont,A,cont_pos);% determine all contours
+            [~,hcontour]=contour(haxes,x_cont,y_cont,A,cont_pos);% determine all contours
             set(hcontour,'Fill','on')% fill the space between contours
             set(hcontour,'LineStyle','none')
             hold on
         end
-        [var_p,hcontour_p]=contour(haxes,x_cont,y_cont,A,cont_pos_plus,'k-');% draw the contours for positive values as solid lines
+        [~,~]=contour(haxes,x_cont,y_cont,A,cont_pos_plus,'k-');% draw the contours for positive values as solid lines
         hold on
-        [var_m,hcontour_m]=contour(haxes,x_cont,y_cont,A,cont_pos_min,'--');% draw the contours for negative values as dashed lines
+        [~,hcontour_m]=contour(haxes,x_cont,y_cont,A,cont_pos_min,'--');% draw the contours for negative values as dashed lines
         if isequal(Opacity,1)
             set(hcontour_m,'LineColor',[1 1 1])% draw negative contours in white (better visibility in dark background)
@@ -977 +980 @@
         
         %determine the color scale and map
-        caxis([abscontmin abscontmax])
+        clim([abscontmin abscontmax])
         if strcmp(ColorMap,'grayscale')
             vec=linspace(0,1,(abscontmax-abscontmin)/interval);%define a greyscale colormap with steps interval
@@ -1005 +1008 @@
                     A=uint8(255*double(A)/double(MaxA));
                 end
-%             otherwise
-%                 colormap(ColorMap);
+            otherwise
+                colormap(ColorMap);
         end
   
@@ -1088 +1091 @@
             end
             if length(PosColorbar)==4
-                set(hcol,'Position',PosColorbar)
+                % set(hcol,'Units','pixel')
+                 set(hcol,'Position',PosColorbar)
             end
             %YTick=0;%default
@@ -1126 +1130 @@
     end
 else%no scalar plot
-    if ~isempty(hima) && ishandle(hima)
+    if  ishandle(hima)
         delete(hima)
     end
-    if ~isempty(PosColorbar) && ~isempty(hcol)&& ishandle(hcol)
+    if ~isempty(PosColorbar) && ~isempty(hcol) && ishandle(hcol)
         delete(hcol)
     end
@@ -1217 +1221 @@
     % take flags into account: add flag colors to the list of colors
     nbcolor=size(colorlist,1);
-% % %     if test_black 
-% % %        nbcolor=nbcolor+1;
-% % %        colorlist(nbcolor,:)=[0 0 0]; %add black to the list of colors
-% % %        if ~isempty(ivar_FF_vec)
-% % %             col_vec(vec_F~=1 & vec_F~=0 & vec_FF==0)=nbcolor;
-% % %        else
-% % %             col_vec(vec_F~=1 & vec_F~=0)=nbcolor;
-% % %        end
-% % %     end
     nbcolor=nbcolor+1;
     if ~isempty(ivar_FF_vec)
@@ -1349 +1344 @@
     arrowplus=rot*[uc;vc];
     arrowmoins=rot'*[uc;vc];
-    % x1=xc+uc/2-arrowplus(1,:);
-    % x2=xc+uc/2;
-    % x3=xc+uc/2-arrowmoins(1,:);
-    % y1=yc+vc/2-arrowplus(2,:);
-    % y2=yc+vc/2;
-    % y3=yc+vc/2-arrowmoins(2,:);
     x1=xc+uc-arrowplus(1,:);
     x2=xc+uc;
@@ -1366 +1355 @@
     matyar=reshape(matyar,1,4*n(2));
     %draw the line or modify the existing ones
-%     tri=reshape(1:3*length(uc),3,[])';   
     isn=isnan(colorlist(icolor,:));%test if color NaN
     if 2*icolor > sizh(1) %if icolor exceeds the number of existing ones
@@ -1432 +1420 @@
 diffy=diff(vec_Y); %difference dy=vec_Y(i+1)-vec_Y(i)
 index=find(diffy);% find the indices of vec_Y after wich a change of horizontal line occurs(diffy non zero)
-if isempty(index); msgbox_uvmat('ERROR','points aligned along abscissa in proj_grid.m'); return; end;%points aligned% A FAIRE: switch to line plot.
+if isempty(index); msgbox_uvmat('ERROR','points aligned along abscissa in proj_grid.m'); return; end%points aligned% A FAIRE: switch to line plot.
 diff2=diff(diffy(index));% diff2 = fluctuations of the detected vertical grid mesh dy 
 if max(abs(diff2))>0.001*abs(diffy(index(1))) % if max(diff2) is larger than 1/1000 of the first mesh dy
@@ -1489 +1477 @@
     end
     if test_interp==1%if we interpolate
-        xi=[rangx(1):(rangx(2)-rangx(1))/(npxy(2)-1):rangx(2)];
-        yi=[rangy(1):(rangy(2)-rangy(1))/(npxy(1)-1):rangy(2)];
+        xi=rangx(1):(rangx(2)-rangx(1))/(npxy(2)-1):rangx(2);
+        yi=rangy(1):(rangy(2)-rangy(1))/(npxy(1)-1):rangy(2);
         [XI,YI]=meshgrid(xi,yi);
         A = interp2(X,Y,B,XI,YI);

trunk/src/series.m

@@ -165 +165 @@
 RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
 if isfield(SeriesData.ClusterParam, 'ExistenceTest')
-    oarcommand=SeriesData.ClusterParam.ExistenceTest;
-    s=system(oarcommand); % look for cluster system presence
+    ClusterExistenceTest=SeriesData.ClusterParam.ExistenceTest;
+    disp('look for cluster command available')
+    s=system(ClusterExistenceTest); % look for cluster system presence
     if isequal(s,0)% cluster detected
         RunModeList=[RunModeList;{'cluster'}];
@@ -568 +569 @@
 %------------------------------------------------------------------------
 CheckRelabel=get(handles.Relabel,'Value');
-check_input_file_series(handles,CheckRelabel)
-
-%% enable field and veltype menus, in accordance with the current action
+errormsg=check_input_file_series(handles,CheckRelabel);
+if ~isempty(errormsg)
+    msgbox_uvmat('ERROR',errormsg);% no input files entered
+    set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
+    return
+end
+
+%% enable field and veltype menus, in accordance with the current action function
 ActionInput_Callback([],[], handles)
 
 %------------------------------------------------------------------------
 % --- check the input file series.
-function check_input_file_series(handles,CheckRelabel)
+function errormsg=check_input_file_series(handles,CheckRelabel)
 %------------------------------------------------------------------------
 InputTable=get(handles.InputTable,'Data');%read the table of input file series
 set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
 set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
-set(handles.Relabel,'BackgroundColor',[0 1 0])
 drawnow
-empty_line=false(size(InputTable,1),1);
+errormsg='';%default
+
+%% removes possible  empty lines in the tables documenting the files index series
+check_empty_line=false(size(InputTable,1),1);
 for iline=1:size(InputTable,1)
-    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));%check the empty lines in the input table
-end
-if ~isempty(find(empty_line,1))%removes the empty lines in the table
-    InputTable(empty_line,:)=[]; % remove empty lines
+    check_empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));%check the empty lines in the input table
+end
+empty_lines=find(check_empty_line);%line indices which are empty
+if numel(empty_lines)==size(InputTable,1)
+   errormsg='input files needed';% no input files
+    return
+end
+if ~isempty(empty_lines)
+    InputTable(empty_lines,:)=[]; % remove empty lines
     set(handles.InputTable,'Data',InputTable)
     ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
     for ilist=1:numel(ListTable)
         Table=get(handles.(ListTable{ilist}),'Data');
-        Table(empty_line,:)=[]; % remove empty lines
+        Table(empty_lines,:)=[]; % remove empty lines
         set(handles.(ListTable{ilist}),'Data',Table);
     end
     set(handles.series,'UserData',[])%refresh the stored info
 end
-nbview=size(InputTable,1);
-CheckRelabelQuest=false;
+nbview=size(InputTable,1);% number of lines filled in the Input file table after this cleaning of empty lines
+
+%% get info on each line of the input table
+CheckRelabelQuest=true;% will ask for relabeling if relevant
 for iview=1:nbview
-    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
-    Param.Relabel=false;
+    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});% path of the input file series
+    Param.Relabel=false;% no relabeling by default
     MovieObject=[];
     Param.FileInfo=[];
     if ~exist(RootPath,'dir')
         Param.i1_series=[];
-        RootFile='';
+        RootFile='';% input folder does not exist, will ask by browser
     else
-        [XmlFileName,Rank]=find_imadoc(InputTable{iview,1},InputTable{iview,2});
+        [XmlFileName,Rank]=find_imadoc(InputTable{iview,1},InputTable{iview,2});%look for ImaDoc file
         if ~isempty(XmlFileName)
-            XmlData=read_imadoc(XmlFileName);
-            if  Rank==0 && ~isempty(XmlData.FileSeries)
-                set(handles.Relabel,'Visible','on')
+            XmlData=read_imadoc(XmlFileName);%read the imadoc file through the local fct read_imadoc
+            if  Rank==0 && ~isempty(XmlData.FileSeries)% file relabeling proposed in the xml file
+                set(handles.Relabel,'Visible','on')% make the relabel check box visible
                 answer='Yes';
-                if ~CheckRelabel && ~CheckRelabelQuest% propose to relabel if not selected yet
+                if ~CheckRelabel && CheckRelabelQuest% propose to relabel if not selected yet
                     answer=msgbox_uvmat('INPUT_Y-N','relabel the frame  indices according to the xml info?');
-                    CheckRelabelQuest=true;
+                    CheckRelabelQuest=false;% will validate the answer for all lines
                 end
-                if strcmp(answer,'Yes')
-                    set(handles.Relabel,'Value',1)
+                if strcmp(answer,'Yes')% relabel option activated
+                    set(handles.Relabel,'Value',1)% activate the relabel option
+                    CheckRelabel=true;
                     NomType='*';
                     i1=1;i2=[];j1=1;j2=[];
@@ -633 +649 @@
                     FirstFile=fullfile(InputTable{iview,1},InputTable{iview,2},XmlData.FileSeries.FileName{1});
                     if ~exist(FirstFile,'file')
-                        msgbox_uvmat('ERROR',[FirstFile ' does not exist']);
+                        errormsg=[FirstFile ' set by the xml file does not exist'];
                         return
                     end
-                    [Param.FileInfo,VideoObject]=get_file_info(FirstFile);
+                    Param.FileInfo=get_file_info(FirstFile);
                 else
-                    set(handles.Relabel,'Value',0)
+                    set(handles.Relabel,'Value',0) % suppress the relabel option
                 end
             end
@@ -647 +663 @@
         %scan the input folder
         InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');%suppress '/' at the beginning of the input name
-        i1=str2double(get(handles.num_first_i,'String'));
-        j1=str2double(get(handles.num_first_j,'String'));
-        j2=[];%default
-%         PairString=get(handles.PairString,'Data');
-%         if numel(PairString)>=iview
-%             r=regexp(PairString{iview},'(?<num1>\d+)-(?<num2>\d+)' ,'names');
-%             if ~isempty(r)
-%                 j1=str2double(r.num1);
-%                 j2=str2double(r.num2);
-%             end
-%         end
- InputFile=[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}];
-        %InputFile=fullfile_uvmat('','',InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1,[],j1,j2);
+        InputFile=[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}];
         [RootPath,~,RootFile,Param.i1_series,Param.i2_series,Param.j1_series,Param.j2_series,~,Param.FileInfo,MovieObject]=...
             find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),InputFile);
     end
 
-    % if no file is found on line #ivew, open a browser
+    % if no file is found on line #iview, open a browser
     if ~Param.Relabel && isempty(RootFile)&& isempty(Param.i1_series)
         fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
         if isempty(fileinput)
-            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
+            errormsg='no input file entered';
             return
         else
-            display_file_name(handles,fileinput,iview)% update the table of input file series, then call update_rootinfo
+            display_file_name(handles,fileinput,iview)% update the table of input file series #iview, then will call update_rootinfo
         end
     else
@@ -678 +682 @@
 end
 
-%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
+%% suppress possible remaining data beyond nbview lines in MinIndex_i, MaxIndex_i ,MinIndex_j, MaxIndex_j,PairString,TimeTable
 MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
-set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
+set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview)); % save only the nbviews values, remove possible values beyond
+
 MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
-set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
-MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
-
-set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
+set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview));
+
+MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the max indices in the table MinIndex
+set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview));
+
 MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
-set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
+set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview));
+
 PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
-set(handles.PairString,'Data',PairString(1:nbview,:));
+set(handles.PairString,'Data',PairString(1:nbview));
+
 TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
 set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
 
-
 set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
 set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
-
 
 
@@ -750 +756 @@
 XmlData=[];
 if ~isempty(XmlFileName)
-    XmlData=read_imadoc(XmlFileName);
+    XmlData=read_imadoc(XmlFileName);%read the imadoc file through the local fct read_imadoc
     if isfield(XmlData,'FileSeries') && Rank==0
         set(handles.Relabel,'Visible','on')
@@ -925 +931 @@
     SeriesData.InputPath=InputPath;
 end
-
-
 set(handles.series,'UserData',SeriesData)
-
 set(handles.InputTable,'BackgroundColor',[1 1 1])
-
-
 
 %% initiate input file series and refresh the current field view:
@@ -947 +948 @@
 % --- get info from the xml file XmlFileName
 function XmlData=read_imadoc(XmlFileName)
-
+%------------------------------------------------------------------------
 [XmlData,errormsg]=imadoc2struct(XmlFileName);
 if ~isempty(errormsg)
@@ -1011 +1012 @@
     if isempty(i1_series)
         MinIndex_j=1;MaxIndex_j=1;MinIndex_i=1;MaxIndex_i=1;
-    elseif size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
+    elseif size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0 % file series with a single index i
         MinIndex_j=1; % index j set to 1 by default
         MaxIndex_j=1;
@@ -1026 +1027 @@
         diff_i_max=diff(ref_i);
         if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
-            set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
+            set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to display by default
         end
         if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
@@ -1078 +1079 @@
         InputTable=get(handles.InputTable,'Data');
         [XmlFileName,Rank]=find_imadoc(InputTable{iview,1},InputTable{iview,2});
-        if isempty(XmlFileName)
-            return
-        else
+        if ~isempty(XmlFileName)
             Param.XmlData=read_imadoc(XmlFileName);
-        end
-        [nbfield,nbfield_j]=size(Param.XmlData.Time);
-        nbfield=nbfield-1; %remove the possible index 0
-        nbfield_j=nbfield_j-1; %remove the possible index 0
-%         MaxIndex_i=get(handles.MaxIndex_i,'Data');
-%         MaxIndex_j=get(handles.MaxIndex_j,'Data');
-%         MaxIndex_i(1,:)=nbfield;
-%         MaxIndex_j(1,:)=nbfield_j;
-%         MinIndex_i(1,:)=1;
-%         MinIndex_j(1,:)=1;
-         MaxIndex_i=nbfield;
-         MaxIndex_j=nbfield_j;
-         MinIndex_i=1;
-         MinIndex_j=1;
-
+            [nbfield,nbfield_j]=size(Param.XmlData.Time);
+            nbfield=nbfield-1; %remove the possible index 0
+            nbfield_j=nbfield_j-1; %remove the possible index 0
+            MaxIndex_i=nbfield;
+            MaxIndex_j=nbfield_j;
+            MinIndex_i=1;
+            MinIndex_j=1;
+        end
 
         first_i=str2double(get(handles.num_first_i,'String'));
@@ -1115 +1107 @@
 
 %% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
-if ~isempty(TimeName)
+if isempty(TimeName)
+    TimeMin=NaN;    TimeMax=NaN;  TimeFirst=NaN;    TimeLast=NaN;
+else
     if size(Time)<[MaxIndex_i+1 MaxIndex_j+1]
-        msgbox_uvmat('WARNING',['incomplete time info in xml file']);
+        msgbox_uvmat('WARNING','incomplete time info in xml file');
     end
     TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
@@ -1143 +1137 @@
 set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
 
-if isfield(Param.XmlData,'NbSlice') && ~isempty(Param.XmlData.NbSlice)
+if isfield(Param,'XmlData') && isfield(Param.XmlData,'NbSlice') && ~isempty(Param.XmlData.NbSlice)
     set(handles.num_NbSlice,'String',num2str(Param.XmlData.NbSlice))
     set(handles.num_NbSlice,'Visible','on')
@@ -1223 +1217 @@
 SeriesData.j1_series{iview}=j1_series;
 SeriesData.j2_series{iview}=j2_series;
-%     SeriesData.FileType{iview}=FileInfo.FileType;
 SeriesData.FileInfo{iview}=Param.FileInfo;
 SeriesData.Time{iview}=Time;
@@ -1882 +1875 @@
         drawnow
     end
-    if get(handles.Replicate,'Value')
+    if get(handles.Replicate,'Value')%resset the input file settings in case of replicated processing
         set(handles.InputTable,'Data',Param.InputTable)
         set(handles.OutputPath,'String',OutputPath)
@@ -2416 +2409 @@
 %------------------------------------------------------------------------
 % --- read parameters from the GUI series
-%------------------------------------------------------------------------
 function Param=read_GUI_series(handles)
-
-%% read raw parameters from the GUI series
+%------------------------------------------------------------------------
+
+% read raw parameters from the GUI series
 Param=read_GUI(handles.series);
 
@@ -2559 +2552 @@
 set(handles.num_CPUTime,'String','')
 
+%------------------------------------------------------------------------
 % --- Executes on button press in ActionInput.
 function ActionInput_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 
 set(handles.ActionInput,'BackgroundColor',[1 1 0])
@@ -3093 +3088 @@
 end
 
-
+%------------------------------------------------------------------------
 function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
+%------------------------------------------------------------------------
 [i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
 FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
@@ -3182 +3178 @@
 end
 
-
-%%%%%%%%%%%%%
+%------------------------------------------------------------------------
 function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
+%------------------------------------------------------------------------
 indsel=ind_i;
 indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
@@ -3307 +3303 @@
 %------------------------------------------------------------------------
 % --- Executes on button press in ViewObject.
-%------------------------------------------------------------------------
 function ViewObject_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 
 UserData=get(handles.series,'UserData');
@@ -3360 +3356 @@
 %------------------------------------------------------------------------
 % --- Executed when CheckMask is activated
-%------------------------------------------------------------------------
 function CheckMask_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 % SeriesData=get(handles.series,'UserData');
 
@@ -3484 +3480 @@
 %------------------------------------------------------------------------
 % --- Executes when selected cell(s) is changed in MaskTable.
-%------------------------------------------------------------------------
 function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
-
+%------------------------------------------------------------------------
 if numel(eventdata.Indices)>=1
 set(handles.ListMask,'Value',eventdata.Indices(1))
@@ -3494 +3489 @@
 function MenuHelp_Callback(hObject, eventdata, handles)
 %-------------------------------------------------------------------
-
-
-% path_to_uvmat=which ('uvmat'); % check the path of uvmat
-% pathelp=fileparts(path_to_uvmat);
-% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
-% if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
-% else
-%     addpath (fullfile(pathelp,'uvmat_doc'))
-%     web([helpfile '#series'])
-% end
+web('https://legi.gricad-pages.univ-grenoble-alpes.fr/soft/uvmat-doc/help')
 
 %-------------------------------------------------------------------
@@ -3580 +3566 @@
 %------------------------------------------------------------------------
 % --- fct activated by the upper bar menu ExportConfig
-%------------------------------------------------------------------------
 function MenuDisplayConfig_Callback(hObject, eventdata, handles)
-
+%------------------------------------------------------------------------
 global Param
 Param=read_GUI_series(handles);
 evalin('base','global Param')%make CurData global in the workspace
-display('current series config :')
+disp('current series config :')
 evalin('base','Param') %display CurData in the workspace
 commandwindow; % brings the Matlab command window to the front
@@ -3595 +3580 @@
 %------------------------------------------------------------------------
 function MenuImportConfig_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 
 %% use a browser to choose the xml file containing the processing config
@@ -3668 +3654 @@
 
 %------------------------------------------------------------------------
-% --- Executes when the GUI series is resized.
-%------------------------------------------------------------------------
+% --- Executes when the GUI series is resized.-
 function series_ResizeFcn(hObject, eventdata, handles)
-
-%% input table
+%------------------------------------------------------------------------
+
+% input table
 set(handles.InputTable,'Unit','pixel')
 Pos=get(handles.InputTable,'Position');
@@ -3713 +3699 @@
 set(handles.PairString,'ColumnWidth',{Pos(3)-5})
 
-%% MaskTable
-% % set(handles.MaskTable,'Unit','pixel')
-% % Pos=get(handles.MaskTable,'Position');
-% % set(handles.MaskTable,'Unit','normalized')
-% % set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
-
-%------------------------------------------------------------------------
-% --- Executes on button press in status.
-%------------------------------------------------------------------------
+%------------------------------------------------------------------------
+% --- Executes on button press in status.-
 function status_Callback(hObject, eventdata, handles)
-
+%------------------------------------------------------------------------
 if get(handles.status,'Value')
     set(handles.status,'BackgroundColor',[1 1 0])
@@ -3752 +3731 @@
 end
 
-
 %------------------------------------------------------------------------
 % launched by selecting a file on the list
-%------------------------------------------------------------------------
 function view_file(hObject, eventdata)
-
+%------------------------------------------------------------------------
 list=get(hObject,'String');
 index=get(hObject,'Value');
@@ -3794 +3771 @@
 end
 
-
 %------------------------------------------------------------------------
 % launched by refreshing the status figure
-%------------------------------------------------------------------------
 function refresh_GUI(hfig)
-
+%------------------------------------------------------------------------
 htitlebox=findobj(hfig,'tag','titlebox');
 hlist=findobj(hfig,'tag','list');
@@ -3858 +3833 @@
 %------------------------------------------------------------------------
 % --- Executes on selection change in ActionExt.
-%------------------------------------------------------------------------
 function ActionExt_Callback(hObject, eventdata, handles)
-
+%------------------------------------------------------------------------
 ActionExtList=get(handles.ActionExt,'String');
 ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
@@ -3912 +3886 @@
 menu=menu(imin:imax);
 
-
-% --- Executes on mouse motion over figure - except title and menu.
-% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
-% set(hObject,'Pointer','arrow');
-
-
+%------------------------------------------------------------------------
 % --- Executes on button press in SetPairs.
 function SetPairs_Callback(hObject, eventdata, handles)
-
+%------------------------------------------------------------------------
 %% delete previous occurrence of 'set_pairs'
 hfig=findobj(allchild(0),'Tag','set_pairs');
@@ -4006 +3975 @@
 %------------------------------------------------------------------------
 function ListView_Callback(hObject,eventdata)
+%------------------------------------------------------------------------
 Mode_Callback(hObject,eventdata)
 
 %------------------------------------------------------------------------
 function Mode_Callback(hObject,eventdata)
+%------------------------------------------------------------------------
 %% get input info
 hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
@@ -4025 +3996 @@
 
 %% enable j index visibility after the new choice
-
 if strcmp(mode,'series(Dj)')
    status_j='on'; % default
@@ -4073 +4043 @@
 set(hPairString,'Data',PairString)
 
-
 %------------------------------------------------------------------------
 function num_ref_i_Callback(hObject, eventdata)
@@ -4089 +4058 @@
 delete(get(hObject,'parent'))
 
-
 %------------------------------------------------------------------------
 % --- Executes on button press in ClearLine.
-%------------------------------------------------------------------------
 function ClearLine_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 InputTable=get(handles.InputTable,'Data');
 iline=str2double(get(handles.InputLine,'String'));
@@ -4102 +4070 @@
 set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
 
-
+%------------------------------------------------------------------------
 % --- Executes on button press in MonitorCluster.
 function MonitorCluster_Callback(hObject, eventdata, handles)
-
+%------------------------------------------------------------------------
 [rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
 if isempty(ss)
@@ -4114 +4082 @@
 end
 
-
+%------------------------------------------------------------------------
 function OutputSubDir_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
 
@@ -4124 +4093 @@
 % --- Executes on button press in TestCPUTime.
 function TestCPUTime_Callback(hObject, eventdata, handles)
-% hObject    handle to TestCPUTime (see GCBO)
-% eventdata  reserved - to be defined in a future version of MATLAB
-% handles    structure with handles and user data (see GUIDATA)
-
-
+
+%------------------------------------------------------------------------
 % --- Executes on button press in DiskQuota.
 function DiskQuota_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 SeriesData=get(handles.series,'UserData');
 system(SeriesData.DiskQuotaCmd)
 
-
+%------------------------------------------------------------------------
 % --- Executes on button press in Replicate.
 function Replicate_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 if get(handles.Replicate,'Value')
     InputTable=get(handles.InputTable,'Data');
@@ -4159 +4127 @@
 function Device_Callback(hObject, eventdata, handles)
 
-
+%------------------------------------------------------------------------
 % --- Executes on button press in OutputPathBrowse.
 function OutputPathBrowse_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 CheckValue=get(handles.OutputPathBrowse,'Value');
 if CheckValue
@@ -4171 +4140 @@
 end
 
-
+%------------------------------------------------------------------------
 % --- Executes on button press in DeleteMask.
 function DeleteMask_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 set(handles.MaskTable,'Data',{})
 
-
+%------------------------------------------------------------------------
 % --- Executes on button press in Relabel.
 function Relabel_Callback(hObject, eventdata, handles)
+%------------------------------------------------------------------------
 CheckRelabel=get(hObject,'Value');
 if CheckRelabel
@@ -4195 +4166 @@
     end
 end
-check_input_file_series(handles,CheckRelabel)
-ActionInput_Callback([],[], handles)
-
-
+check_input_file_series(handles,CheckRelabel)% check the min and max relabeled indices, or original ones if CheckRelabel=false
+ActionInput_Callback([],[], handles)% %% enable menus (field, vel type,...), in accordance with the current action function
+
+

trunk/src/series.xml.default

@@ -6 +6 @@
       <NbCoreAdvised>16</NbCoreAdvised>                        <!-- proposed default number of parallel cores attributed for the computations -->
       <NbCoreMax>36</NbCoreMax>                                <!-- maximum number of cores allowed for the computations -->
-      <JobCPUTimeAdvised unit="minute">20</JobCPUTimeAdvised>  <!-- used to group the iterations into jobs of sufficient CPU time -->
+      <JobCPUTimeAdvised unit="minute">60</JobCPUTimeAdvised>  <!-- used to group the iterations into jobs of sufficient CPU time -->
       <JobNumberMax>500</JobNumberMax>                         <!-- maximum number of jobs allowed (will group the iterations to fit in) -->
       <WallTimeMax unit="hour">23</WallTimeMax>                <!-- maximum allowed time for a job -->

trunk/src/series/civ_input.m

@@ -89 +89 @@
 FileType='image';%fdefault
 FileInfo=[];
-if isfield(SeriesData,'FileInfo')
+if isfield(SeriesData,'FileInfo') && ~isempty(SeriesData.FileInfo)
     FileType=SeriesData.FileInfo{1}.FileType;% info on the first input file series
 else

trunk/src/series/civ_series.m

@@ -392 +392 @@
             [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B);
             
-        % catch ME % display errors in reading input images
-        %     if ~isempty(ME.message)
-        %         disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
-        %         continue
-        %     end
-        % end
         
         % case of background image to subtract
         if par_civ1.CheckBackground &&~isempty(par_civ1.Background)
             [RootPath_background,SubDir_background,RootFile_background,~,~,~,~,Ext_background]=fileparts_uvmat(Param.ActionInput.Civ1.Background);
-            if ~isempty(i2_series_Civ1)% case of volume,backgrounds act on different j levels
+            if strcmp(NomTypeNc,'_1-2_1')% case of volume,backgrounds act on different j levels
                 backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',j1_series_Civ1(ifield));
-            elseif isfield(par_civ1,'NbSlice')
+            elseif isfield(par_civ1,'NbSlice')&& ~isequal(par_civ1.NbSlice,1)
                 i1_background=mod(i1-1,par_civ1.NbSlice)+1;
                 backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',i1_background);
@@ -418 +412 @@
                 if ~isempty(regexp(backgroundname,'(^http://)|(^https://)', 'once'))|| exist(backgroundname,'file')
                     try
-                        par_civ1.Background=imread(backgroundname);%update the background, an store it for future use
+                        par_civ1.Background=uint16(imread(backgroundname));%update the background, an store it for future use
                     catch ME
                         if ~isempty(ME.message)
@@ -432 +426 @@
                 backgroundoldname=backgroundname;
             end
-            par_civ1.ImageA=par_civ1.ImageA-par_civ1.Background;
-            par_civ1.ImageB=par_civ1.ImageB-par_civ1.Background;
+            par_civ1.ImageA=uint16(par_civ1.ImageA)-par_civ1.Background;
+            par_civ1.ImageB=uint16(par_civ1.ImageB)-par_civ1.Background;
         end
         
@@ -496 +490 @@
             if ~isempty(i2_series_Civ1)&& ~isequal(i1_series_Civ1,i2_series_Civ1)% case of volume,masks act on different j levels
                 maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',j1);
-            elseif isfield(par_civ1,'NbSlice')
+            elseif isfield(par_civ1,'NbSlice')&& ~isequal(par_civ1.NbSlice,1)
                 i1_mask=mod(i1-1,par_civ1.NbSlice)+1;
                 maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
@@ -638 +632 @@
         if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A,FrameIndex_A_2)
             par_civ2.ImageA=par_civ1.ImageA;
+            CheckDuplicate_1to2A=true;
         else
             [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_2);
+            CheckDuplicate_1to2A=false;
         end
         if CheckRelabel
@@ -650 +646 @@
         if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_2,FrameIndex_B)
             par_civ2.ImageB=par_civ1.ImageB;
+            CheckDuplicate_1to2B=true;
         else
             [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_2);
+             CheckDuplicate_1to2B=false;
         end
         %  [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2);
@@ -673 +671 @@
         end
         
-        %                 %% user defined image transform
-        %         if ~isempty(transform_fct)
-        %                par_civ2 =transform_fct(par_civ2,Param);
-        %         end
+        %% case of background image to subtract, if images civ2 different from civ1
+        if (~CheckDuplicate_1to2A || ~CheckDuplicate_1to2B) && par_civ2.CheckBackground &&~isempty(par_civ2.Background)
+            [RootPath_background,SubDir_background,RootFile_background,~,~,~,~,Ext_background]=fileparts_uvmat(Param.ActionInput.Civ2.Background);
+            j1=1;
+            if ~isempty(j1_series_Civ2)
+                j1=j1_series_Civ2(ifield);
+            end
+            if ~isempty(i2_series_Civ2)% case of volume,backgrounds act on different j levels
+                backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',j1);
+            elseif isfield(par_civ2,'NbSlice') && ~isequal(par_civ2.NbSlice,1)
+                i1_background=mod(i1-1,par_civ2.NbSlice)+1;
+                backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',i1_background);
+                if strcmp(Param.ActionInput.PairIndices.ListPairMode,'series(Di)')% case of volume, background index refers to j index
+                    par_civ2.NbSlice_j=par_civ2.NbSlice;
+                end
+            else
+                backgroundname=Param.ActionInput.Civ2.Background;
+            end
+            if strcmp(backgroundoldname,backgroundname)% background exist, not already read in civ2
+                par_civ2.Background=background; %use background already opened
+            else
+                if ~isempty(regexp(backgroundname,'(^http://)|(^https://)', 'once'))|| exist(backgroundname,'file')
+                    try
+                        par_civ2.Background=uint16(imread(backgroundname));%update the background, an store it for future use
+                    catch ME
+                        if ~isempty(ME.message)
+                            errormsg=['error reading input image: ' ME.message];
+                            disp_uvmat('ERROR',errormsg,checkrun)
+                            return
+                        end
+                    end
+                else
+                    par_civ2.Background=[];
+                end
+                background=par_civ2.Background;
+                backgroundoldname=backgroundname;
+            end
+            if ~CheckDuplicate_1to2A
+            par_civ2.ImageA=uint16(par_civ2.ImageA)-par_civ2.Background;
+            end
+            if ~CheckDuplicate_1to2B
+            par_civ2.ImageB=uint16(par_civ2.ImageB)-par_civ2.Background;
+            end
+        end
+   
         %% case of image luminosity rescaling
-        if par_civ2.CheckRescale &&~isempty(par_civ2.Maxtanh)
-            par_civ2.ImageA =par_civ2.Maxtanh*tanh(double(par_civ2.ImageA)/par_civ2.Maxtanh);
-            par_civ2.ImageB=par_civ2.Maxtanh*tanh(double(par_civ2.ImageB)/par_civ2.Maxtanh);
+        if  par_civ2.CheckRescale && ~isempty(par_civ2.Maxtanh)
+            if ~CheckDuplicate_1to2A %if the image A is different from civ1
+                par_civ2.ImageA =par_civ2.Maxtanh*tanh(double(par_civ2.ImageA)/par_civ2.Maxtanh);
+            end
+            if ~CheckDuplicate_1to2B % if the image B is different from civ1
+                par_civ2.ImageB=par_civ2.Maxtanh*tanh(double(par_civ2.ImageB)/par_civ2.Maxtanh);
+            end
         end
         
@@ -761 +804 @@
                 end
                 maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',j1);
-            elseif isfield(par_civ2,'NbSlice')
+            elseif isfield(par_civ2,'NbSlice')&& ~isequal(par_civ2.NbSlice,1)
                 i1=i1_series_Civ2(ifield);
                 i1_mask=mod(i1-1,par_civ2.NbSlice)+1;
@@ -794 +837 @@
         end
         
-        % case of background image to subtract
-        if par_civ2.CheckBackground &&~isempty(par_civ2.Background)
-            [RootPath_background,SubDir_background,RootFile_background,~,~,~,~,Ext_background]=fileparts_uvmat(Param.ActionInput.Civ1.Background);
-            j1=1;
-            if ~isempty(j1_series_Civ1)
-                j1=j1_series_Civ1(ifield);
-            end
-            if ~isempty(i2_series_Civ1)% case of volume,backgrounds act on different j levels
-                backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',j1);
-            elseif isfield(par_civ2,'NbSlice')
-                i1_background=mod(i1-1,par_civ2.NbSlice)+1;
-                backgroundname=fullfile_uvmat(RootPath_background,SubDir_background,RootFile_background,Ext_background,'_1',i1_background);
-                if strcmp(Param.ActionInput.PairIndices.ListPairMode,'series(Di)')% case of volume, background index refers to j index
-                    par_civ2.NbSlice_j=par_civ2.NbSlice;
-                end
-            else
-                backgroundname=Param.ActionInput.Civ1.Background;
-            end
-            if strcmp(backgroundoldname,backgroundname)% background exist, not already read in civ2
-                par_civ2.Background=background; %use background already opened
-            else
-                if ~isempty(regexp(backgroundname,'(^http://)|(^https://)', 'once'))|| exist(backgroundname,'file')
-                    try
-                        par_civ2.Background=imread(backgroundname);%update the background, an store it for future use
-                    catch ME
-                        if ~isempty(ME.message)
-                            errormsg=['error reading input image: ' ME.message];
-                            disp_uvmat('ERROR',errormsg,checkrun)
-                            return
-                        end
-                    end
-                else
-                    par_civ2.Background=[];
-                end
-                background=par_civ2.Background;
-                backgroundoldname=backgroundname;
-            end
-            par_civ2.ImageA=par_civ2.ImageA-par_civ2.Background;
-            par_civ2.ImageB=par_civ2.ImageB-par_civ2.Background;
-        end
-        
+        %% get civ2 correlation parameters
         if strcmp(Param.ActionInput.ListCompareMode,'displacement')
             Civ1_Dt=1;
@@ -852 +855 @@
         end
         
-        % calculate velocity data (y and v in image indices, reverse to y component)
-        
+        % calculate velocity data      
         [Civ_X,Civ_Y,Civ_U,Civ_V,Civ_C,Civ_FF,~, errormsg] = civ (par_civ2);
         Civ_X_shifted=Civ_X-0.5+Civ_U/2;% get the exact positions
@@ -878 +880 @@
         Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
         
-        %        nbvar=numel(Data.ListVarName);
-        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
-        %         if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
-        %             Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_C','Civ2_FF'}];%  cell array containing the names of the fields to record
-        %             Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
-        %             Data.VarAttribute{nbvar+1}.Role='coord_x';
-        %             Data.VarAttribute{nbvar+2}.Role='coord_y';
-        %             Data.VarAttribute{nbvar+3}.Role='vector_x';
-        %             Data.VarAttribute{nbvar+4}.Role='vector_y';
-        %             Data.VarAttribute{nbvar+5}.Role='ancillary';
-        %             Data.VarAttribute{nbvar+6}.Role='errorflag';
-        %         end
         disp('civ2 performed')
         time_civ2=toc(tstart_civ2);
@@ -930 +920 @@
         end
         Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
-        
-        %  nbvar=length(Data.ListVarName);
-        %         Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
-        %         Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
-        %             {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
-        
-        %         Data.VarAttribute{nbvar+1}.Role='vector_x';
-        %         Data.VarAttribute{nbvar+2}.Role='vector_y';
-        %         Data.VarAttribute{nbvar+5}.Role='coord_tps';
-        %         Data.VarAttribute{nbvar+6}.Role='vector_x';
-        %         Data.VarAttribute{nbvar+7}.Role='vector_y';
         
         if isempty(Civ_FF)

trunk/src/uvmat.m

@@ -192 +192 @@
 LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
 set(hObject,'Position',[LeftX LowY Width Height])
-UvData.PosColorbar=[0.80 0.02 0.018 0.445];
+%UvData.PosColorbar=[0.80 0.02 0.018 0.445];
 AxeData.LimEditBox=1; %initialise AxeData
 set(handles.PlotAxes,'UserData',AxeData)
@@ -221 +221 @@
 %% EXPORT menu
 export_menu={'as field in workspace';'in new figure';'on existing axis';'make movie';'more...'};
-%export_path=fullfile(path_uvmat,'export_fct');
 
 %% load the list of previously browsed files in menus Open, Open_1 and TransformName
@@ -264 +263 @@
 set(handles.TransformPath,'String','')
 set(handles.TransformPath,'UserData',[])
-export_menu=[export_menu;{'more...'}];%append the option more.. to the menu
+%export_menu=[export_menu;{'more...'}];%append the option more.. to the menu
 
 %% case of an input argument for uvmat
@@ -295 +294 @@
         UvData.Field.coord_x=[0.5 size(input,2)-0.5];
         UvData.Field.coord_y=[size(input,1)-0.5 0.5];
-        %testinputfield=1;
     end
 else
     %% check the path and date of modification of all functions in uvmat
     path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
-    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m
+    [infomsg,date_str]=check_files;%check the path of the functions called by uvmat.m
     date_str=['last modification: ' date_str];
     if ishandle(handles.UVMAT_title)
@@ -357 +355 @@
 %------------------------------------------------------------------------
 set(handles.uvmat,'Units','pixels')
-size_fig=get(handles.uvmat,'Position');
-ColumnWidth=max(150,0.18*size_fig(3)); %width of the right side display column equal to 0.18 *uvmat_GUI, in the range between 150 px and 250 px
+size_uvmat=get(handles.uvmat,'Position');
+ColumnWidth=max(150,0.18*size_uvmat(3)); %width of the right side display column equal to 0.18 *uvmat_GUI, in the range between 150 px and 250 px
 ColumnWidth=min(ColumnWidth,250);
-
-%% position of panel InputFile
+InputFilePanelHeight=80;
+TextDisplayPanelHeight=100;
+CheckTablePanelHeight=100;
+CoordinatesPanelHeight=100;
+ScalarPanelHeight=150;
+Interval=2;
+
+%% reset position of panel InputFile
 set(handles.InputFile,'Units','pixels')
 %pos_InputFile=get(handles.InputFile,'Position')% [lower x lower y width height] for text_display
-pos_InputFile(1)=0;            % set frame InputFile to the left of uvmat GUI
-pos_InputFile(2)=size_fig(4)-60;             % set frame InputFile to the top of uvmat GUI
-pos_InputFile(3)=size_fig(3);     %width of the GUI uvmat
-pos_InputFile(4)=60; %set the height of the panel to 60 px
+pos_InputFile(1)=Interval;            % set frame InputFile to the left of uvmat GUI
+pos_InputFile(2)=size_uvmat(4)-InputFilePanelHeight-Interval;             % set frame InputFile to the top of uvmat GUI
+pos_InputFile(3)=size_uvmat(3)-2*Interval;     %width of the GUI uvmat
+pos_InputFile(4)=InputFilePanelHeight; %set the height of the panel 
 set(handles.InputFile,'Position',pos_InputFile);% [lower x lower y width height] 
 
@@ -373 +377 @@
 set(handles.text_display,'Units','pixels')
 set(handles.TableDisplay,'Units','pixels')
-pos_1=get(handles.text_display,'Position');% [lower x lower y width height] for text_display
-pos_1(3)=1.2*ColumnWidth;
-pos_1(1)=size_fig(3)-pos_1(3);             % set text display to the right of the fig
-pos_1(2)=size_fig(4)-pos_InputFile(4)-pos_1(4);             % set text display to the top of the fig
+pos_1(1)=size_uvmat(3)-ColumnWidth-Interval;
+pos_1(2)=pos_InputFile(2)-TextDisplayPanelHeight-Interval;             % set text display to the top of the fig
+pos_1(3)=ColumnWidth;
+pos_1(4)=TextDisplayPanelHeight;          
 set(handles.text_display,'Position',pos_1)
 set(handles.TableDisplay,'Position',[pos_1(1) 10 pos_1(3) 5*pos_1(4)])
-% reset position of CheckTable
+
+%% reset position of CheckTable 
 set(handles.CheckTable,'Units','pixels')
-pos_CheckTable=get(handles.CheckTable,'Position');% [lower x lower y width height] for CheckHold
-pos_CheckTable(1)=pos_1(1)-pos_CheckTable(3);       % set 'CheckHold' to the right of the fig
-pos_CheckTable(2)=pos_InputFile(2)-pos_CheckTable(4);          % set 'CheckHold' to the lower edge of text display
+pos_CheckTable(1)=size_uvmat(3)-ColumnWidth-Interval;       % set 'CheckHold' to the right of the fig
+pos_CheckTable(2)=pos_InputFile(2)-CheckTablePanelHeight-Interval;          % set 'CheckHold' to the lower edge of text display
+pos_CheckTable(3)=ColumnWidth; 
+pos_CheckTable(4)=CheckTablePanelHeight; 
 set(handles.CheckTable,'Position',pos_CheckTable)
-
-%% reset position of CheckHold
-% pos_CheckHold=get(handles.CheckHold,'Position');% [lower x lower y width height] for CheckHold
-% pos_CheckHold(1)=size_fig(3)-pos_CheckHold(3);       % set 'CheckHold' to the right of the fig
-% pos_CheckHold(2)=pos_1(2)-pos_CheckHold(4);          % set 'CheckHold' to the lower edge of text display
-% set(handles.CheckHold,'Position',pos_CheckHold)
 
 %% reset position of Coordinates panel
 set(handles.Coordinates,'Units','pixels')
-%pos_2=get(handles.Coordinates,'Position')% [lower x lower y width height] for frame 'Coordinates'
-pos_2(1)=size_fig(3)-ColumnWidth;       % set 'Coordinates' to the right of the fig
-pos_2(2)=pos_1(2)-80;          % set 'Coordinates' to the lower edge of text display
+pos_2(1)=size_uvmat(3)-ColumnWidth-Interval;       % set 'Coordinates' to the right of the fig
+pos_2(2)=pos_1(2)-CoordinatesPanelHeight-Interval;          % set 'Coordinates' to the lower edge of text display
 pos_2(3)=ColumnWidth;
-pos_2(4)=80;%keep height to 80 px
+pos_2(4)=CoordinatesPanelHeight;%keep height to 80 px
 set(handles.Coordinates,'Position',pos_2)
 
 %% reset position of Axes panel
 set(handles.Axes,'Units','pixels')
-%pos_3=get(handles.Axes,'Position')% [lower x lower y width height] for frame 'Coordinates'
-pos_3(1)=size_fig(3)-ColumnWidth;       % set 'Coordinates' to the right of the fig
-pos_3(2)=pos_2(2)-140;   
+pos_3(1)=size_uvmat(3)-ColumnWidth-Interval;       % set 'Coordinates' to the right of the fig
+pos_3(2)=pos_2(2)-140-Interval;   
 pos_3(3)=ColumnWidth;
 pos_3(4)=140;%keep height to 140 px
@@ -412 +410 @@
 %% reset position of  Scalar
 set(handles.Scalar,'Units','pixels')
-%pos_4=get(handles.Scalar,'Position') % [lower x lower y width height] for frame 'Scalar'
-pos_4(1)=size_fig(3)-ColumnWidth;         % set 'Scalar' to the right of the fig
+pos_4(1)=size_uvmat(3)-ColumnWidth-Interval;         % set 'Scalar' to the right of the fig
 if strcmp(get(handles.Scalar,'Visible'),'on')
-    pos_4(2)=pos_3(2)-140; % set 'Scalar' to the lower edge of frame 'Coordinates' if visible
-else
-    pos_4(2)=pos_3(2);% set 'Scalar' to the lower edge of frame 'text display' if  unvisible
+    pos_4(2)=pos_3(2)-ScalarPanelHeight-Interval; % set 'Scalar' to the lower edge of frame 'Coordinates' if visible
+else
+    pos_4(2)=pos_3(2)-Interval;% set 'Scalar' to the lower edge of frame 'text display' if  unvisible
 end
 pos_4(3)=ColumnWidth;
-pos_4(4)=140;
+pos_4(4)=ScalarPanelHeight;
 set(handles.Scalar,'Position',pos_4)
 
 %% reset position of  Vectors
 set(handles.Vectors,'Units','pixels')
-%pos_5=get(handles.Vectors,'Position')
-pos_5(1)=size_fig(3)-ColumnWidth;
+pos_5(1)=size_uvmat(3)-ColumnWidth-Interval;
 if strcmp(get(handles.Vectors,'visible'),'on')
-    pos_5(2)=pos_4(2)-240;
-else
-    pos_5(2)=pos_4(2);
+    pos_5(2)=pos_4(2)-240-Interval;
+else
+    pos_5(2)=pos_4(2)-Interval;
 end
 pos_5(3)=ColumnWidth;
@@ -437 +433 @@
 
 %% reset position and scale of axis
-pos(1)=0.2*size_fig(3)+35;
+pos(1)=0.2*size_uvmat(3)+35;
 pos(2)=50;
-pos(3)=0.77*size_fig(3)-1.2*ColumnWidth;
-pos(4)=size_fig(4)-100;
+pos(3)=0.77*size_uvmat(3)-1.2*ColumnWidth;
+pos(4)=pos_InputFile(2)-50-Interval;
 set(handles.PlotAxes,'Units','pixels')
 set(handles.PlotAxes,'Position',pos)
-set(handles.PlotAxes,'Units','normalized')
-
-
+%set(handles.PlotAxes,'Units','normalized')
+UvData=get(handles.uvmat,'UserData');
+UvData.PosColorbar([1 3])=[pos(1)+pos(3)+10 10]/size_uvmat(3);
+UvData.PosColorbar([2 4])=[pos(2)+pos(3)/4 pos(3)/2]/size_uvmat(4);
+set(handles.uvmat,'UserData',UvData)
+
+%% reset position of Field Indices TODO
+% set(handles.FieldIndices,'Units','pixels')
+% pos_4(1)=size_uvmat(3)-ColumnWidth;         % set 'Scalar' to the right of the fig
+% if strcmp(get(handles.Scalar,'Visible'),'on')
+%     pos_4(2)=pos_3(2)-ScalarPanelHeight-Interval; % set 'Scalar' to the lower edge of frame 'Coordinates' if visible
+% else
+%     pos_4(2)=pos_3(2)-Interval;% set 'Scalar' to the lower edge of frame 'text display' if  unvisible
+% end
+% pos_4(3)=ColumnWidth;
+% pos_4(4)=ScalarPanelHeight;
+% set(handles.Scalar,'Position',pos_4)
 
 %------------------------------------------------------------------------
@@ -2119 +2129 @@
 function MenuHelp_Callback(hObject, eventdata, handles)
 % --------------------------------------------------------------------
-web('https://gricad-gitlab.univ-grenoble-alpes.fr/legi/soft/uvmat-doc/-/blob/master/help/README.md')
+web('https://legi.gricad-pages.univ-grenoble-alpes.fr/soft/uvmat-doc/help')
 
 
@@ -3015 +3025 @@
     end
     FileInfo=get_file_info(fileinput);
-    if isfield(FileInfo,'MaskFile')%&& exist(FileInfo.MaskFile,'file')
+    if isfield(FileInfo,'MaskFile') % if a Mask has been documented in the input file (civ data)
         Mask.MaskFile=FileInfo.MaskFile;
         if isfield(FileInfo,'MaskNbSlice')
             Mask.MaskNbSlice=FileInfo.MaskNbSlice;
         end
-    else
+    else % look for an apporpriate mask with the browser
         filemask= uigetfile_uvmat('pick a mask image file:',fileinput,'image');
         if ~isempty(filemask)
             [FilePath,FileName,FileExt]=fileparts(filemask);
-            [RootPath,SubDir,RootFile,i1_series,i2,j1,j2,NomType]=find_file_series(FilePath,[FileName FileExt]);
+            [RootPath,SubDir,RootFile,i1_series,~,~,~,NomType]=find_file_series(FilePath,[FileName FileExt]);
             if strcmp(NomType,'_1')
                 Mask.MaskFile=fullfile(RootPath,SubDir,RootFile);
                 Mask.MaskExt=FileExt;
                 Mask.MaskNbSlice=i1_series(1,2,end);
-            elseif ~strcmp(NomType,'*')
+            elseif strcmp(NomType,'*')
+                Mask.MaskFile=fullfile(RootPath,SubDir,RootFile);
+                Mask.MaskExt=FileExt;
+            else
                 msgbox_uvmat('ERROR','multilevel masks must be labeled with a single index as _1,_2,...');
                 set(handles.CheckMask,'Value',0)
@@ -3036 +3049 @@
         end
     end
-    %         i1=str2double(get(handles.num_i1,'String'));
-    %         filemask=FileInfo.MaskFile;
-    %         if isfield(FileInfo,'MaskNbSlice')
-    %         i1=str2double(get(handles.num_i1,'String'));
-    %         MaskIndex=mod(i1,FileInfo.MaskNbSlice)
-    %         filemask=[filemask '_' num2str(MaskIndex) FileInfo.MaskExt]
-    % %     else
-    % %         filemask= uigetfile_uvmat('pick a mask image file:',RootPath,'image');
-    %     end
-    %     if ~isempty(filemask)
-    %         [MaskPath,FileName,FileExt]=fileparts(filemask);
-    %         Mask.File=filemask;
-    %         [~,~,~,i1_series,~,~,~,NomType]=find_file_series(MaskPath,[FileName FileExt]);
-    %         Mask.NbSlice=[];%default
-    %         Mask.VolumeScan=0;% TO UPDATE ***
-    %         if strcmp(NomType,'_1')
-    %             Mask.NbSlice=i1_series(1,2,end);
-    %             set(handles.num_NbSlice,'String',num2str(Mask.NbSlice))
-    %         elseif ~strcmp(NomType,'*')
-    %             msgbox_uvmat('ERROR','multilevel masks must be labeled with a single index as _1,_2,...');
-    %             return
-    %         end
-    %set(hObject,'UserData',filemask);%store for future use
     set(handles.CheckMask,'UserData',Mask);
     errormsg=update_mask(handles);
@@ -3083 +3073 @@
 %------------------------------------------------------------------------
 errormsg=[];%default
-MaskName='';
+%MaskName='';
 
 %% get the current mask name recorded in CheckMask/UserData, possibly indexed with file index
@@ -3089 +3079 @@
 if isfield(MaskInfo,'MaskFile')
     if isfield(MaskInfo,'MaskNbSlice')&& ~isempty(MaskInfo.MaskNbSlice)
-        if isfield(MaskInfo,'VolumeScan') &&  MaskInfo.VolumeScan
+        if isfield(MaskInfo,'VolumeScan') &&  MaskInfo.VolumeScanTransformMenu
             MaskIndex_i=str2double(get(handles.num_j1,'String'));
         else
@@ -3097 +3087 @@
     else
         MaskIndex_i=1;
-        MaskName=MaskInfo.MaskFile;
+    MaskName=[MaskInfo.MaskFile MaskInfo.MaskExt];
     end
     
     %% update mask image if the mask is new
     UvData=get(handles.uvmat,'UserData');
-     TransformMenu=get(handles.TransformName,'String')
+     TransformMenu=get(handles.TransformName,'String');
       TransformName=  TransformMenu{get(handles.TransformName,'Value')};
     if ~ (isfield(UvData,'MaskName') && strcmp(UvData.MaskName,MaskName)&& isfield(UvData,'TransformName')&& strcmp(UvData.TransformName,TransformName))%check if the mask is new
@@ -3108 +3098 @@
         UvData.TransformName=TransformName; %update the recorded name on UvData
         set(handles.uvmat,'UserData',UvData);
-        if exist(MaskName,'file')~=2
+        if exist(MaskName,'file')~=2 % case file MaskName does not exist
             if isfield(MaskInfo,'maskhandle')&& ishandle(Mask.maskhandle)
                 delete(MaskInfo.maskhandle)
+                set(handles.CheckMask,'Value',0)
             end
         else
@@ -3322 +3313 @@
     set(handles.CheckFixPair,'Value',0)
 end
-%CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(num_i2)&& isempty(num_j2));
 
 % the pair num_i1-num_i2 or num_j1-num_j2 is imposed (check box CheckFixPair selected)
@@ -3427 +3417 @@
             ref_j_1=ref_j;
         end
-        if numel(UvData.i1_series)==1
+        if isscalar(UvData.i1_series)
             UvData.i1_series{2}=UvData.i1_series{1};
             UvData.j1_series{2}=UvData.j1_series{1};
@@ -3503 +3493 @@
         NbField_j_cell=get(handles.MaxIndex_j,'String');
         NbField_j=str2double(NbField_j_cell{1});
-        [RootFile,FrameIndex]=index2filename(UvData.XmlData{1}.FileSeries,i1,j1,NbField_j);
+        RootFile=index2filename(UvData.XmlData{1}.FileSeries,i1,j1,NbField_j);
         [~,RootFile]=fileparts(RootFile);%suppress the file extension
         set(handles.RootFile,'String',RootFile)
@@ -4133 +4123 @@
     check_x_name=find(strcmp(coord_x_name,UvData.Field.ListVarName));
     UvData.Field.VarAttribute{check_x_name}.Role='coord_x';
-    [PlotType,PlotParamOut,haxes]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
+    [~,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
     UvData.PlotAxes=UvData.Field; %store data for further plot modifications
     errormsg=fill_GUI(PlotParamOut,handles.uvmat);
@@ -4312 +4302 @@
             else
                 [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap});
-                if ~isempty(regexp(PlotType,'^error'))%exit in case of plotting error
-                    if ~isempty(regexp(PlotType,'attempt to plot two vector fields'))
+                if ~isempty(regexp(PlotType,'^error', 'once'))%exit in case of plotting error
+                    if ~isempty(regexp(PlotType,'attempt to plot two vector fields', 'once'))
                         set(handles.CheckEditObject,'Value',1)
                         CheckEditObject_Callback([], [], handles)% propose to edit the main projection plane
@@ -5654 +5644 @@
 %-------------------------------------------------------------------
 function num_Opacity_Callback(hObject, eventdata, handles)
+%-------------------------------------------------------------------
 update_plot(handles);
-%-------------------------------------------------------------------
 
 %-------------------------------------------------------------------
@@ -5709 +5699 @@
 %------------------------------------------------------------------------
 % --- Executes on selection change in CheckDecimate4 (nb_vec/4).
-%------------------------------------------------------------------------
 function CheckDecimate4_Callback(hObject, eventdata, handles)
-
+%------------------------------------------------------------------------
 if isequal(get(handles.CheckDecimate4,'Value'),1)
     set(handles.CheckDecimate16,'Value',0)