Index: trunk/src/series/aver_stat.m
===================================================================
--- trunk/src/series/aver_stat.m	(revision 27)
+++ trunk/src/series/aver_stat.m	(revision 29)
@@ -32,5 +32,4 @@
 WaitbarPos=get(hseries.waitbar_frame,'Position');
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
 %root input file and type
 if ~iscell(Series.RootPath)% case of a single input field series
@@ -235,34 +234,35 @@
 
 % Root name of output files (TO GENERALISE FOR TWO INPUT SERIES)
-filebasesub=fullfile(RootPath{1},SubDir{1},RootFile{1});
-if isempty(SubDir{1}) % create a subdirectory '/mean'
-    subdir_result='mean';
+subdir_result='aver_stat';
+% filebasesub=fullfile(RootPath{1},subdir_result,RootFile{1});
+% if isempty(SubDir{1}) % create a subdirectory '/aver_stat'
+%     subdir_result='aver_stat';
 %     filebasemean=fullfile(RootPath{1},subdir_result);
-    if ~exist(fullfile(RootPath{1},subdir_result),'dir')
-        dircur=pwd; %record current working directory
-        cd(RootPath{1})% goes to the iamge directory
-        [m1,m2,m3]=mkdir(subdir_result);
-        if ~isequal(m2,'')
-             msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation
-        end
-        cd(dircur) %back to the initial working directory
-    end
-    filebase_out=filebase{1}; 
-else
-   subdir_result=SubDir{1};
-   filebase_out=[filebase{1} '_mean'];% output root name obtained by adding the suffix _mean to the input
-end
+if ~exist(fullfile(RootPath{1},subdir_result),'dir')
+    dircur=pwd; %record current working directory
+    cd(RootPath{1})% goes to the iamge directory
+    [m1,m2,m3]=mkdir(subdir_result);
+    if ~isequal(m2,'')
+         msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation
+    end
+    cd(dircur) %back to the initial working directory
+end
+filebase_out=filebase{1}; 
+% else
+%    subdir_result=SubDir{1};
+%    filebase_out=[filebase{1} '_mean'];% output root name obtained by adding the suffix _mean to the input
+% end
 %output nomtype (to generalise)
 NomTypeOut=nomtype2pair(NomType{1},num_i2{end}(end)-num_i1{1}(1),num_j2{end}(end)-num_j1{1}(1));
     
-if NbSlice==1  
-    filebase_out=[filebasesub '_mean'];
-else
-    filebase_out=[filebasesub '_' NbSlice_name 'mean'];
-    answeryes=questdlg({['will make average in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_out ' ...']});
-    if ~isequal(answeryes,'Yes')
-        return
-    end
-end
+% if NbSlice==1  
+%     filebase_out=[filebasesub '_mean'];
+% else
+%     filebase_out=[filebasesub '_' NbSlice_name 'mean'];
+%     answeryes=questdlg({['will make average in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_out ' ...']});
+%     if ~isequal(answeryes,'Yes')
+%         return
+%     end
+% end
 
 % coordinate transform or other user defined transform
@@ -394,9 +394,9 @@
     %writing the result file
    if testima   
-       if NbSlice==1
-        [filemean]=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.png',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end));
-       else % label the file number by the slice # for simplicity
-          [filemean]=name_generator(filebase_out,i_slice,1,'.png','_i');
-       end
+%        if NbSlice==1
+        [filemean]=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.png',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end),subdir_result);
+%        else % label the file number by the slice # for simplicity
+%           [filemean]=name_generator(filebase_out,i_slice,1,'.png','_i');
+%        end
         if exist(filemean,'file')
             backupfile=filemean;
@@ -429,9 +429,9 @@
             DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {'Time','Time_end'}];
         end  
-        if NbSlice==1
-          filemean=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.nc',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end));
-        else % label the file number by the slice # for simplicity
-          [filemean]=name_generator(filebase_out,i_slice,1,'.nc','_i');
-        end
+%         if NbSlice==1
+          filemean=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.nc',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end),subdir_result);
+%         else % label the file number by the slice # for simplicity
+%           [filemean]=name_generator(filebase_out,i_slice,1,'.nc','_i');
+%         end
         if exist(filemean,'file')
             backupfile=filemean;
@@ -459,4 +459,3 @@
 hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI
 delete(hget_field)
-'TEST'
 uvmat(filemean)
Index: trunk/src/series/merge_proj.m
===================================================================
--- trunk/src/series/merge_proj.m	(revision 29)
+++ trunk/src/series/merge_proj.m	(revision 29)
@@ -0,0 +1,383 @@
+function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series);
+
+%requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
+if ~exist('num_i1','var')
+    GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
+        'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
+        'RootFile';'on';... %root input file name ('on' by default)
+        'FileExt';'on';... %input file extension ('on' by default)
+        'NomType';'on';...%type of file indexing ('on' by default)
+        'NbSlice';'on'; ...%nbre of slices ('off' by default)
+        'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default)
+        'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
+        'CoordType';'on';...%can use a transform function 'off' by default
+        'GetObject';'on';...%can use projection object ,'off' by default
+        %'GetMask';'on'...%can use mask option   ,'off' by default
+        %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter 
+               ''};
+    return %exit the function 
+end
+
+%-------------------------------------------------
+hseries=guidata(Series.hseries);%handles of the GUI series
+WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame
+%-------------------------------------------------
+
+%numbers of view fields (nbre of inputs in RootPath)
+testcell=iscell(Series.RootFile);
+if ~testcell
+    Series.RootPath={Series.RootPath};
+    Series.RootFile={Series.RootFile};
+    Series.SubDir={Series.SubDir};
+    Series.FileExt={Series.FileExt};
+    Series.NomType={Series.NomType};
+    num_i1={num_i1};
+    num_i2={num_i2};
+    num_j1={num_j1};
+    num_j2={num_j2};
+end 
+nbview=length(Series.RootFile);%number of views (file series to merge)
+nbfield=size(num_i1{1},1)*size(num_i1{1},2);%number of fields in the time series
+transform=Series.CoordType; %  field transform function
+hhh=which('mmreader');
+for iview=1:nbview
+    test_movie(iview)=0;
+    if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
+        if isequal(lower(FileExt{iview}),'.avi')
+            MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}]));
+            test_movie(iview)=1;
+        end
+    end 
+end
+
+%Calibration data and timing: read the ImaDoc files
+mode=''; %default
+timecell={};
+itime=0;
+NbSlice_calib={}; %test for z index 
+for iview=1:nbview%Loop on views
+    XmlData{iview}=[];%default
+    filebase{iview}=fullfile(Series.RootPath{iview},Series.RootFile{iview});
+    if exist([filebase{iview} '.xml'],'file')
+        [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); 
+        if isfield(XmlData{iview},'Time')
+            itime=itime+1;
+            timecell{itime}=XmlData{iview}.Time;
+        end
+        if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord')
+            NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);
+            if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
+                msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
+            end
+        end    
+    elseif exist([filebase{iview} '.civ'],'file')
+        [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']);
+        itime=itime+1;
+        timecell{itime}=time;
+        XmlData{iview}.Time=time;
+        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
+        GeometryCalib.Tx=0;
+        GeometryCalib.Ty=0;
+        GeometryCalib.Tz=1;
+        GeometryCalib.dpx=1;
+        GeometryCalib.dpy=1;
+        GeometryCalib.sx=1;
+        GeometryCalib.Cx=0;
+        GeometryCalib.Cy=0;
+        GeometryCalib.f=1;
+        GeometryCalib.kappa1=0;
+        GeometryCalib.CoordUnit='cm';
+        XmlData{iview}.GeometryCalib=GeometryCalib;
+        if error==1
+            msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
+        end
+    end
+end
+
+%check coincidence in time
+multitime=0;
+if length(timecell)==0
+    time=[];
+elseif length(timecell)==1
+    time=timecell{1};
+elseif length(timecell)>1
+    multitime=1;
+    for icell=1:length(timecell)
+        if ~isequal(size(timecell{icell}),size(timecell{1}))
+            msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used')
+            time=timecell{1};
+            multitime=0;
+            break
+        end
+    end
+end
+if multitime
+    for icell=1:length(timecell)
+        time(icell,:,:)=timecell{icell};
+    end
+    diff_time=max(max(diff(time)));
+    if diff_time>0
+        msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)])
+    end   
+end
+if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' 
+    time=[];
+end
+
+% Field and velocity type (the same for all views)
+Field_str=get(hseries.FieldMenu,'String');
+val=get(hseries.FieldMenu,'Value');
+FieldName=Field_str(val);%the same set of fields for all views
+VelType_str=get(hseries.VelTypeMenu,'String');
+VelType_val=get(hseries.VelTypeMenu,'Value');
+VelType=VelType_str{VelType_val}; %the same for all views
+if isequal(FieldName,'get_field...')
+    hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
+   % hhget_field=guidata(hget_field);%handles of GUI elements in get_field
+    SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI
+%     if isequal(get(hhget_field.menu_coord,'Visible'),'on')
+%         list_transform=get(hhget_field.menu_coord,'String');
+%         val_list=get(hhget_field.menu_coord,'Value');
+%         transform=list_transform{val_list};
+%     end
+end
+%detect whether all the files are 'images' or 'netcdf'
+testima=0;
+testvol=0;
+testcivx=0;
+testnc=0;
+FileExt=get(hseries.FileExt,'String');
+for iview=1:nbview
+     ext=FileExt{iview};
+     form=imformats(ext([2:end]));
+     if isequal(lower(ext),'.vol')
+         testvol=testvol+1;
+     elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab
+         testima=testima+1;
+     elseif isequal(ext,'.nc')
+         testnc=testnc+1;
+     end
+end
+if testvol
+    msgbox_uvmat('ERROR','volume images not implemented yet')
+    return
+end
+if testnc~=nbview && testima~=nbview && testvol~=nbview
+    msgbox_uvmat('ERROR','need a set of images or a set of netcdf files with the same fields as input')
+    return
+end
+if ~isequal(FieldName,'get_field...')
+    testcivx=testnc;
+end
+%name of output files and directory:
+% res_subdir=fullfile(Series.RootPath{1},[Series.SubDir{1} '_STAT']);
+ProjectDir=fileparts(fileparts(Series.RootPath{1}));% preoject directory (GERK)
+prompt={['result directory (in' ProjectDir ')']};
+RootPath=get(hseries.RootPath,'String');
+SubDir=get(hseries.SubDir,'String');
+if isequal(length(RootPath),1)
+    fulldir=RootPath{1};
+    subdir='GRID';
+    res_subdir=fullfile(fulldir,subdir);
+else
+    def={fullfile(ProjectDir,'0_RESULTS')};
+    dlgTitle='result directory';
+    lineNo=1;
+    answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def);
+    fulldir=answer{1};
+    subdir=[];
+    dirlist=sort(Series.RootFile);
+    for iview=1:nbview
+        if ~isempty(subdir)
+            subdir=[subdir '-'];
+        end
+        subdir=[subdir dirlist{iview}];
+    end  
+    res_subdir=fullfile(fulldir,subdir);
+end
+ext=FileExt{1};
+if ~exist(fulldir,'dir')
+    msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created'])
+    return
+end
+if ~exist(res_subdir,'dir')
+    dircur=pwd;
+    cd(fulldir)
+    error=mkdir(subdir);
+    cd(dircur)
+end
+filebasesub=fullfile(res_subdir,Series.RootFile{1});
+filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files
+
+%projection object
+if isfield(Series,'sethandles')
+    if ishandle(Series.sethandles.set_object)
+        Series.ProjObject=read_set_object(Series.sethandles);
+        if ~isfield(Series.ProjObject,'Style')
+            msgbox_uvmat('ERROR','Undefined projection object style')
+            return
+        end
+        if ~isequal(Series.ProjObject.Style,'plane')
+            msgbox_uvmat('ERROR','The projection object must be a plane')
+            return
+        end
+    end
+end
+
+    %MAIN LOOP
+for ifile=1:nbfield                
+    stopstate=get(hseries.RUN,'BusyAction');
+    if isequal(stopstate,'queue')% enable STOP command from the 'series' interface
+         update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield)
+         Amerge=0;
+         
+         %----------LOOP ON VIEWS----------------------
+        nbtime=0;
+        for iview=1:nbview
+            %name of the current file
+            filename=name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview});
+            if ~exist(filename,'file')
+                msgbox_uvmat('ERROR',['missing input file' filename])
+                break
+            end
+
+            %reading the current file
+            if testima
+                if test_movie(iview)
+                    Field{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile));
+                else
+                    Field{iview}.A=read_image(filename,Series.NomType{iview},num_i1{iview}(ifile)); 
+                end % TODO: introduce ListVarName
+                npxy=size(Field{iview}.A);
+                Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
+                Field{iview}.AY=[npxy(1)-0.5 0.5];
+                Field{iview}.CoordType='px'; 
+                Field{iview}.AName='image';
+            else
+                if testcivx
+                    [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType);
+                else
+                    [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data                
+                    Field{iview}.VarAttribute=SubField.VarAttribute;
+                end
+                if isfield(Field{iview},'Time')
+                    timeread(iview)=Field{iview}.Time;
+                    nbtime=nbtime+1;
+                end
+            end
+            % coord transform
+            % z index
+            if ~isempty(NbSlice_calib)
+                Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1;
+            end
+            if ~isequal(transform,'')
+                Field{iview}=feval(Series.CoordType,Field{iview},XmlData{iview});%transform to phys if requested
+            end
+            if testcivx
+                    Field{iview}=calc_field(FieldName,Field{iview});
+            end
+
+            %projection on object (gridded plane)
+            if isfield(Series,'ProjObject')
+                Field{iview}=proj_field(Field{iview},Series.ProjObject);
+            end
+        end    
+        
+         %----------END LOOP ON VIEWS----------------------
+         
+        %merge the nbview fields
+        MergeData=merge_field(Field);
+        if isfield(MergeData,'Txt')
+            msgbox_uvmat('ERROR',MergeData.Txt)
+            return
+        end
+        
+        % generating the name of the merged field
+        mergename=name_generator(filebase_merge,num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile));
+        
+        % time:
+        time_i=0;%default
+        if isempty(time)% time from ImaDoc prevails
+            time_i=sum(timeread)/nbtime;
+        else
+            time_i=(time(iview,num_i1{iview}(ifile),num_j1{iview}(ifile))+time(iview,num_i2{iview}(ifile),num_j2{iview}(ifile)))/2;
+        end
+        
+        % recording the merged field
+        if testima    %in case of input images an image is produced   
+            if isa(MergeData.A,'uint8')
+                bitdepth=8;
+            elseif isa(MergeData.A,'uint16')
+                bitdepth=16;
+            end
+            imwrite(MergeData.A,mergename,'BitDepth',bitdepth); 
+            %write xml calibration file
+            siz=size(MergeData.A);
+            npy=siz(1);
+            npx=siz(2);
+            if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1')
+                Rangx=MergeData.VarAttribute{1}.Coord_2;
+                Rangy=MergeData.VarAttribute{1}.Coord_1;
+            elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
+                Rangx=[MergeData.AX(1) MergeData.AX(end)];
+                Rangy=[MergeData.AY(1) MergeData.AY(end)];
+            else
+                Rangx=[0.5 npx-0.5];
+                Rangy=[npy-0.5 0.5];%default
+            end
+            pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
+            pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
+            T_x=-pxcmx*Rangx(1)+0.5;
+            T_y=-pxcmy*Rangy(2)+0.5;
+            GeometryCal.focal=1;
+            GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
+            GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
+            ImaDoc.GeometryCalib=GeometryCal;
+            t=struct2xml(ImaDoc);
+            t=set(t,1,'name','ImaDoc');
+            save(t,[filebase_merge '.xml'])     
+            display([filebase_merge '.xml saved'])
+        else
+            MergeData.ListGlobalAttribute={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'};        
+            MergeData.nb_coord=2;
+            MergeData.nb_dim=2;
+            MergeData.dt=1;
+            MergeData.Time=time_i;
+            error=struct2nc(mergename,MergeData); %save result file
+            if isempty(error)
+                display(['output file ' mergename ' written'])
+            else
+                display(error)
+            end
+        end
+    end
+end
+
+%--------------------------------------------------------------------------   
+function MergeData=merge_field(Data)
+% initiate Matlab  structure for physical field
+if isempty(Data)||~iscell(Data)
+    MergeData=[];
+    return
+end
+MergeData=Data{1};%default
+error=0;
+nbview=length(Data);
+if nbview==1
+    return
+end
+for iview=1:nbview
+    if ~isequal(MergeData.ListDimName,Data{iview}.ListDimName)
+        error=1;
+    end
+    if ~isequal(MergeData.ListVarName,Data{iview}.ListVarName)
+        error=1;
+    end
+%      if ~isequal(MergeData.VarDimIndex,Data{iview}.VarDimIndex)
+%         error=1;
+%      end
+end
+if error
+    MergeData.Txt='ERROR: attempt at merging fields of incompatible type';
+    return
+end
