%'sub_field_series': substract the two input field series, then possibly project them on a grid (like merge_proj;m)
% GUI_input=sub_field_series(num_i1,num_i2,num_j1,num_j2,Series)
%
%OUTPUT
% GUI_input=list of options in the GUI series.fig needed for the function
%
%INPUT:
%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
%Series: Matlab structure containing information set by the series interface
%
function GUI_input=sub_field_series(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
hhh=which('mmreader');
for iview=1:nbview
    test_movie(iview)=0;
    if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
        if isequal(lower(Series.FileExt{iview}),'.avi')
            MovieObject{iview}=mmreader(fullfile(Series.RootPath{iview},[Series.RootFile{iview} Series.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 (nbview=2)
    XmlData{iview}=[];%default
    filebase{iview}=fullfile(Series.RootPath{iview},Series.RootFile{iview});
    testxml(iview)=0;% test for xml file
    if exist([filebase{iview} '.xml'],'file')
        testxml(iview)=1;
        [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   
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

%% coordinate transform or other user defined transform
transform_fct=[];%default
if isfield(Series,'transform_fct')
    transform_fct=Series.transform_fct;
end

%% Field and velocity type (the same for all views)
FieldName='';
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;
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
if nbview~=2
    msgbox_uvmat('ERROR','this function needs two input series as input')
    return
elseif testima
    answer=msgbox_uvmat('CONFIRMATION','this function will substract each of the second image series from the first one');
    if ~isequal(answer,'Yes')
        return
    end
else
    answer=msgbox_uvmat('CONFIRMATION','this function will substract each the second field series from the first one');
    if ~isequal(answer,'Yes')
        return
    end
end


%% name of output files and directory:
ProjectDir=fileparts(fileparts(Series.RootPath{1}));% preoject directory (GERK)
prompt={['result directory (in' ProjectDir ')']};
RootPath=get(hseries.RootPath,'String');
SubDir=get(hseries.SubDir,'String');
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);

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,Series.RootFile{1});
filebase_merge=fullfile(res_subdir,'sub');%root name for the merged files
 if testxml(1) && ( isempty(transform_fct)|| isequal(transform_fct,'px'))
        copyfile([filebase{1} '.xml'],[filebase_merge '.xml'])% reproduce the xml file
        display([filebase_merge '.xml copied from ' filebase{1} '.xml'])
    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)
         
        %% ----------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=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';
                timeread(iview)=0;
            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(num_i1{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}=proj_field(Field{iview},ProjObject);
%             end
        end    
        %----------END LOOP ON VIEWS----------------------
         
        %% merge the nbview=2 fields
        MergeData=sub_field(Field{1},Field{2});
        if isfield(MergeData,'Txt')
            msgbox_uvmat('ERROR',MergeData.Txt)
            return
        end        
        
     % time of the merged field:
        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 
             % generating the name of the merged field
            mergename=name_generator(filebase_merge,num_i1{1}(ifile),num_j1{1}(ifile),'.png',Series.NomType{1},1,num_i2{1}(ifile),num_j2{1}(ifile));
             if isa(Field{1}.A,'uint8')
                imwrite(uint8(MergeData.A),mergename,'BitDepth',8); % transform in integers (and put to 0 the negative values)
             elseif isa(Field{1}.A,'uint16')
                 imwrite(uint16(MergeData.A),mergename,'BitDepth',16);
             end
             display(['output image ' mergename ' written'])
        else
            mergename=name_generator(filebase_merge,num_i1{1}(ifile),num_j1{1}(ifile),'.nc',Series.NomType{1},1,num_i2{1}(ifile),num_j2{1}(ifile));
            MergeData.ListGlobalAttribute={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'};        
            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
%write xml calibration file
if testima && ~isempty(transform_fct) && ~isequal(transform_fct,'px')
    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'])
end