source: trunk/src/series/merge_proj.m @ 457

%'merge_proj': project and concatene fieldsmerge_proj
% can be used as a template for applying an operation (here projection and concateantion) on each field of an input series
%------------------------------------------------------------------------
% function GUI_config=merge_proj(Param)
%------------------------------------------------------------------------

%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function is used in four modes by the GUI series:
%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced. 
%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
%
% This function is used in four modes by the GUI series:
%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced. 
%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
%
%OUTPUT
% GUI_input=list of options in the GUI series.fig needed for the function
%
%INPUT:
% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
% In batch mode, Param is the name of the corresponding xml file containing the same information
% In the absence of input (as activated when the current Action is selected
% in series), the function ouput GUI_input set the activation of the needed GUI elements
%
% Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
%    .InputTable: cell of input file names, (several lines for multiple input)
%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
%    .OutputSubDir: name of the subdirectory for data outputs
%    .OutputDir: directory for data outputs, including path
%    .Action: .ActionName: name of the current activated function
%             .ActionPath:   path of the current activated function
%    .IndexRange: set the file or frame indices on which the action must be performed
%    .FieldTransform: .TransformName: name of the selected transform function
%                     .TransformPath:   path  of the selected transform function
%                     .TransformHandle: corresponding function handle
%    .InputFields: sub structure describing the input fields withfields
%              .FieldName: name of the field
%              .VelType: velocity type
%              .FieldName_1: name of the second field in case of two input series
%              .VelType_1: velocity type of the second field in case of two input series
%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function GUI_input=merge_proj(Param)

%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
if ~exist('Param','var') % case with no input parameter 
    GUI_input={'NbViewMax';2;...% max nbre of input file series (default='' , no limitation)
        'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default)
        'NbSlice';'on'; ...%nbre of slices ('off' by default)
        'VelType';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
        'FieldName';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
        'FieldTransform'; 'on';...%can use a transform function
        'ProjObject';'on';...%can use projection object(option 'off'/'on',
        'Mask';'on';...%can use mask option   (option 'off'/'on', 'off' by default)
        'OutputDirExt';'.proj';...%set the output dir extension
               ''};
        return
end

%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
%% select different modes,  RUN, parameter input, BATCH
% BATCH  case: read the xml file for batch case
if ischar(Param)
    if strcmp(Param,'input?')
        checkrun=1;% will inly search input parameters (preparation of BATCH mode)
    else
        Param=xml2struct(Param);
        checkrun=0;
    end
% RUN case: parameters introduced as the input structure Param
else
    hseries=guidata(Param.hseries);%handles of the GUI series
    WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series
    checkrun=2; % indicate the RUN option is used
end

%% root input file(s) and type
RootPath=Param.InputTable(:,1);
RootFile=Param.InputTable(:,3);
SubDir=Param.InputTable(:,2);
NomType=Param.InputTable(:,4);
FileExt=Param.InputTable(:,5);

% get the set of input file names (cell array filecell), and the lists of
% input file or frame indices i1_series,i2_series,j1_series,j2_series
[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
% filecell{iview,fileindex}: cell array representing the list of file names
%        iview: line in the table corresponding to a given file series
%        fileindex: file index within  the file series, 
% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j 
% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
% set of frame indices used for movie or multimage input 
% numbers of slices and file indices

NbSlice=1;%default
if isfield(Param.IndexRange,'NbSlice')
    NbSlice=Param.IndexRange.NbSlice;
end
nbview=numel(i1_series);%number of input file series (lines in InputTable)
nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
nbfield_i=size(i1_series{1},2); %nb of fields for the i index
nbfield=nbfield_j*nbfield_i; %total number of fields
nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices) 
nbfield=nbfield_i*NbSlice; %total number of fields after adjustement

%determine the file type on each line from the first input file 
ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)

[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1});
CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images
if ~isempty(j1_series{1})
    frame_index{1}=j1_series{1};
else
    frame_index{1}=i1_series{1};
end

%% calibration data and timing: read the ImaDoc files
mode=''; %default
timecell={};
itime=0;
NbSlice_calib={};
for iview=1:nbview%Loop on views
    XmlData{iview}=[];%default
    filebase{iview}=fullfile(RootPath{iview},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);%nbre of slices for Zindex in phys transform
            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 for several input file series
multitime=0;
if isempty(timecell)
    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 (max) ' num2str(diff_time)])
    end   
end
if size(time,2) < i2_series{1}(end) || size(time,3) < j2_series{1}(end)% time array absent or too short in ImaDoc xml file' 
    time=[];
end

%% coordinate transform or other user defined transform
transform_fct='';%default
if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'TransformHandle')
    transform_fct=Param.FieldTransform.TransformHandle;
end
%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
 % EDIT FROM HERE

%% check the validity of  input file types
if CheckImage{1}
    FileExtOut='.png'; % write result as .png images for image inputs
elseif CheckNc{1}
    FileExtOut='.nc';% write result as .nc files for netcdf inputs
else 
    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
    return
end
if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
        msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
    return
end
NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series
if NbSlice~=nbfield_j
    answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]);
    if ~strcmp(answer,'Yes')
        return
    end
end

%% Set field names and velocity types
InputFields{1}=[];%default (case of images)
if isfield(Param,'InputFields')
    InputFields{1}=Param.InputFields;
end
if nbview==2
    InputFields{2}=[];%default (case of images)
    if isfield(Param,'InputFields')
        InputFields{2}=Param.InputFields{1};%default
        if isfield(Param.InputFields,'FieldName_1')
            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
            if isfield(Param.InputFields,'VelType_1')
                InputFields{2}.VelType=Param.InputFields.VelType_1;
            end
        end
    end
end

%% Initiate output fields
%initiate the output structure as a copy of the first input one (reproduce fields)
[DataOut,ParamOut,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1);
if ~isempty(errormsg)
    msgbox_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg])
    return
end
time_1=[];
if isfield(DataOut,'Time')
    time_1=DataOut.Time(1);
end
if CheckNc{iview}
    if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute))
        DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute];
    end
    DataOut.Conventions='uvmat';
    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}];
    ActionKey='Action';
    while isfield(DataOut,ActionKey)
        ActionKey=[ActionKey '_1'];
    end
    DataOut.(ActionKey)=Param.Action;
    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}];
    if isfield(DataOut,'Time')
        DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}];
    end
end

%% MAIN LOOP ON SLICES
%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
for i_slice=1:NbSlice
    index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
    nbfiles=0;
    nbmissing=0;
    
   %initiate result fields
   for ivar=1:length(DataOut.ListVarName)
       DataOut.(DataOut.ListVarName{ivar})=0; % initialise all fields to zero
   end

    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
    for index=index_slice
        if checkrun
            update_waitbar(hseries.waitbar_frame,WaitbarPos,index/(nbfield))
            stopstate=get(hseries.RUN,'BusyAction');
        else
            stopstate='queue';
        end
%OUTPUT
% GUI_input=list of options in the GUI series.fig needed for the function
%
%INPUT:
% Param: structure containing all the parameters read on the GUI series
%  or name of the xml file containing these parameters (BATCH case)
%


%% projection object
test_object=get(hseries.GetObject,'Value');
if test_object
    hset_object=findobj(allchild(0),'tag','set_object');
    %ProjObject=read_set_object(guidata(hset_object));
    ProjObject=read_GUI(hset_object);
    if ~isfield(ProjObject,'Type')
            msgbox_uvmat('ERROR','Undefined projection object type')
            return
    end
    if ~isequal(ProjObject.Type,'plane')|| isequal(ProjObject.ProjMode,'projection')
            msgbox_uvmat('ERROR','The projection object must be a plane with projection mode interp or filter')
            return
    end
    answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type]);
    if ~isequal(answeryes,'Yes')
        return
    end
end

%% features of the input fields
RootPath=Param.InputTable(:,1);
RootFile=Param.InputTable(:,3);
SubDir=Param.InputTable(:,2);
NomType=Param.InputTable(:,4);
FileExt=Param.InputTable(:,5);

nbview=length(RootFile);%number of views (file series to merge)
nbfield=size(i1_series{1},1)*size(i1_series{1},2);%number of fields in the time series
hhh=which('mmreader');
for iview=1:nbview
    test_movie(iview)=0;
    if ~isempty(hhh)
        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
timecell={};
itime=0;
NbSlice_calib={}; %test for z index 
for iview=1:nbview%Loop on views
    XmlData{iview}=[];%default
    filebase{iview}=fullfile(RootPath{iview},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 isempty(timecell)
    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   
    time=sqeeze(mean(time,1));
end
% if size(time,2) < i2_series{1}(end) || size(time,3) < j2_series{1}(end)% ime array absent or too short in ImaDoc xml file' 
%     time=[];
% end

%% Field and velocity type (the same for all views)
FieldName='';
if isfield(Param,'InputFields')&&isfield(Param.InputFields,'FieldMenu')  
    FieldName=Param.InputFields.FieldMenu;%the same set of fields for all views
    VelType=Param.InputFields.VelTypeMenu;
end
% if strcmp(get(hseries.FieldMenu,'Visible'),'on')
%     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 strcmp(FieldName,'')
        msgbox_uvmat('ERROR','no input field defined in FieldMenu')
    elseif strcmp(FieldName,'get_field...')
        hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
        SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI
    end
% end
%detect whether all the files are 'images' or 'netcdf'
testima=0;
testvol=0;
testcivx=0;
testnc=0;
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:
ProjectDir=fileparts(fileparts(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='merge_proj';
    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(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);
    succeed=mkdir(subdir);
    if succeed
        [xx,msg2] = fileattrib(res_subdir,'+w','g'); %yield writing access (+w) to user group (g)
        if ~strcmp(msg2,'')
            msgbox_uvmat('ERROR',['pb of permission for ' res_subdir ': ' msg2])%error message for directory creation
            cd(dircur)
            return
        end
        cd(dircur);
    else
        msgbox_uvmat('ERROR',['Cannot create directory ' fulldir])
        return
    end
end
filebasesub=fullfile(res_subdir,RootFile{1});
%filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files

%% 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)
         
        %% ----------LOOP ON VIEWS----------------------
        nbtime=0;
        for iview=1:nbview
         %name of the current file
         filename=filecell{iview,ifile};
          %  filename=name_generator(filebase{iview},i1_series{iview}(ifile),j1_series{iview}(ifile),FileExt{iview},NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile),SubDir{iview});
            if ~exist(filename,'file')
                msgbox_uvmat('ERROR',['missing input file' filename])
                break
            end
            timeread(iview)=0;
         %reading the current file
            if testima
                if test_movie(iview)
                    Field{iview}.A=read(MovieObject{iview},i1_series{iview}(ifile));
                else
                    Field{iview}.A=imread(filename); 
                end % TODO: introduce ListVarName
                npxy=size(Field{iview}.A);
                Field{iview}.ListVarName={'AX','AY','A'};
                Field{iview}.VarDimName={'AX','AY',{'AY','AX'}};
                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}.CoordUnit='pixel'; 
                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},'Txt')
                    msgbox_uvmat('ERROR',Field{iview}.Txt)
                    return
                end
                if isfield(Field{iview},'Time')
                    timeread(iview)=Field{iview}.Time;
                    nbtime=nbtime+1;
                end
            end
            if ~isempty(NbSlice_calib)
                Field{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1;
            end
         %transform the input field (e.g; phys) if requested
            if ~isempty(transform_fct)
                Field{iview}=transform_fct(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 test_object
                [Field{iview},errormsg]=proj_field(Field{iview},ProjObject);
                if ~isempty(errormsg)
                    msgbox_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg])
                    return
                end
            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
     if testima
         ResultExt='.png';
     else
         ResultExt=FileExt{iview};
     end
     i1=i1_series{iview}(ifile);
     if ~isempty(i2_series{iview})
         i2=i2_series{iview}(ifile);
     else
         i2=i1;
     end
     j1=1;
     j2=1;
     if ~isempty(j1_series{iview})
         j1=j1_series{iview}(ifile);
          if ~isempty(j2_series{iview})
              j2=j2_series{iview}(ifile);
          else
              j2=j1;
          end
     end
     mergename=fullfile_uvmat(res_subdir,'','merged',ResultExt,NomType{iview},i1,i2,j1,j2);
    % mergename=name_generator(filebase_merge,i1,j1_series{iview}(ifile),ResultExt,NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile));
        
     % time of the merged field:
        time_i=0;%default
        if isempty(time)% time from ImaDoc prevails
            time_i=sum(timeread)/nbtime;
        else
           % time_i=i1;
            time_i=(time(i1,j1)+time(i2,j2))/2; %TODO: upgrade
        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={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'};        
            MergeData.Conventions='uvmat';
            MergeData.nb_coord=2;
            MergeData.nb_dim=2;
            dt=[];
            if isfield(Field{1},'dt')&& isnumeric(Field{1}.dt)
                dt=Field{1}.dt;
            end
            for iview =2:numel(Field)
                if ~(isfield(Field{iview},'dt')&& isequal(Field{iview}.dt,dt))
                    dt=[];%dt not the same for all fields
                end
            end
            if isempty(dt)
                MergeData.ListGlobalAttribute(6)=[];
            else
               MergeData.dt=dt;
            end
            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

%'merge_field': concatene fields
%------------------------------------------------------------------------
function MergeData=merge_field(Data)
%% default output
if isempty(Data)||~iscell(Data)
    MergeData=[];
    return
end
MergeData=Data{1};%default
error=0;
nbview=length(Data);
if nbview==1
    return
end

%% group the variables (fields of 'FieldData') in cells of variables with the same dimensions
[CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1});
%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
% CellVarIndex=cells of variable index arrays
ivar_new=0; % index of the current variable in the projected field
for icell=1:length(CellVarIndex)
    if NbDim(icell)==1
        continue
    end
    VarIndex=CellVarIndex{icell};%  indices of the selected variables in the list FieldData.ListVarName
    VarType=VarTypeCell{icell};
    ivar_X=VarType.coord_x;
    ivar_Y=VarType.coord_y;
    ivar_FF=VarType.errorflag;
    if isempty(ivar_X)
        test_grid=1;%test for input data on regular grid (e.g. image)coordinates
    else
        if length(ivar_Y)~=1
                msgbox_uvmat('ERROR','y coordinate missing in proj_field.m')
                return
        end
        test_grid=0;
    end
    %case of input fields with unstructured coordinates
    if ~test_grid
        for ivar=VarIndex
            VarName=MergeData.ListVarName{ivar};
            for iview=1:nbview
                eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName '];'])
            end
        end
    %case of fields defined on a structured  grid 
    else  
        testFF=0;
        for iview=2:nbview
            for ivar=VarIndex
                VarName=MergeData.ListVarName{ivar};
                if isfield(MergeData,'VarAttribute')
                    if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag')
                        testFF=1;
                    end
                end
                eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';'])
            end
        end
        if testFF
            nbaver=nbview-MergeData.FF;
            indgood=find(nbaver>0);
            for ivar=VarIndex
                VarName=MergeData.ListVarName{ivar};
                eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);'])
            end 
        else
            for ivar=VarIndex
                VarName=MergeData.ListVarName{ivar};
                eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;'])
            end    
        end
    end
end