function gyTestAllBF(fname,dFLIMImageData,dFLIMXYTData,dFLIMHistoData)
% dFLIM.ome.tif format
% save a single dFLIM acquisition (contents of a .dFLIM.mat file) to
%   the OME-Tiff format.
% series 0 = dFLIM_Image (XYCTZ, with subchannels of C)
% series 1 = dFLIM_XYT   (XYtCZ)
% series 2 = dFLIM_Histo (xyCTZ, where x=t and y=1)

%% first figure out the sizes and numbers to be saved
sz=size(dFLIMImageData);

% number of Z slices
    szZ=1; % for test

% number of dFLIM channels
    nChan=size(dFLIMImageData,1)/3; % for test

% size of images
szX = size(dFLIMImageData{1,1},1);
szY = size(dFLIMImageData{1,1},2);
nFrames = size(dFLIMImageData,2);

% histo info
nBins = numel(dFLIMHistoData{1,1});

% XYT available?
xytAvail = ~isempty(dFLIMXYTData);
tic;

%% Create metadata

% Fix from Ian Munro for duplicate XML writing
java.lang.System.setProperty('javax.xml.transform.TransformerFactory', ...
    'com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl');

% global state
toInt = @(x) ome.xml.model.primitives.PositiveInteger(java.lang.Integer(x));
OMEXMLService = loci.formats.services.OMEXMLServiceImpl();
metadata = OMEXMLService.createOMEXMLMetadata();
metadata.createRoot();
dimensionOrderEnumHandler = ome.xml.model.enums.handlers.DimensionOrderEnumHandler();
experimentTypeEnumHandler = ome.xml.model.enums.handlers.ExperimentTypeEnumHandler();
experimentType = experimentTypeEnumHandler.getEnumeration('FluorescenceLifetime');
pixelTypeEnumHandler = ome.xml.model.enums.handlers.PixelTypeEnumHandler();

dimOrder = {'XYCTZ', 'XYTCZ', 'XYCTZ'};  % by series

for series=0:2
    sSeries=num2str(series);
    metadata.setImageID(['Image:' sSeries], series);
    metadata.setPixelsID(['Pixels:' sSeries], series);
    metadata.setPixelsBinDataBigEndian (java.lang.Boolean.TRUE, series, 0); % (java.lang.Boolean.TRUE, 0, 0);  NOT SURE ABOUT THIRD PARAMETER USAGE 
    
    % Set dimension order and experiment type for the series
    dimensionOrder = dimensionOrderEnumHandler.getEnumeration(dimOrder{series+1}); % GY (ip.Results.dimensionOrder);
    metadata.setPixelsDimensionOrder(dimensionOrder, series);
    if series==0
        metadata.setExperimentType(experimentType,series);
        % TODO - duplicated header string
        % metadata.setExperimenterID(state.dFLIM.filename,0);
        metadata.setExperimentID('dFLIM_v2.1', series);
        metadata.setExperimentDescription('short description to save space', series); %dF_makeheaderstr, series);
    end
    
    % Set pixels type 
    if series==2
        pixelsType = pixelTypeEnumHandler.getEnumeration('double'); 
    else
        pixelsType = pixelTypeEnumHandler.getEnumeration('uint16'); 
    end
    metadata.setPixelsType(pixelsType, series);
    
    switch series
        case 0  % dFLIMImages
            szXYZCT = [szX szY szZ 3*nChan nFrames];
        case 1  % XYT
            if xytAvail
                szXYZCT = [szX szY szZ nChan nBins];
            else
                szXYZCT = [0 0 0 0 0];
            end
        case 2 % Histos
            szXYZCT = [nBins 1 szZ nChan nFrames];
    end % switch series (size assignment)
    
    metadata.setPixelsSizeX(toInt(szXYZCT(1)), series);
    metadata.setPixelsSizeY(toInt(szXYZCT(2)), series);
    metadata.setPixelsSizeZ(toInt(szXYZCT(3)), series);
    metadata.setPixelsSizeC(toInt(szXYZCT(4)), series);
    metadata.setPixelsSizeT(toInt(szXYZCT(5)), series);
    
    % Set channels ID and samples per pixel
    suffix={':img' ':nmg' ':tmg'};
    for i = 1:nChan
        chID = num2str((i),'%02i');
        if series==0
            for j=1:3
                ch = (i-1)*3+j-1;
                chname = ['dChannel:' chID suffix{j}];
                % chname = ['Channel:' chID(2) ':' num2str(j-1)];
                metadata.setChannelID(chname, series, ch);   % (['Channel:0:' num2str(i-1)], 0, i-1);
                metadata.setChannelFluor(chname, series, ch);
                metadata.setChannelSamplesPerPixel(toInt(1), series, ch);
            end
        else
            ch = (i-1);
            chname = ['dChannel:' chID ];
            metadata.setChannelID(chname, series, ch);   % (['Channel:0:' num2str(i-1)], 0, i-1);
            metadata.setChannelFluor(chname, series, ch);
            metadata.setChannelSamplesPerPixel(toInt(1), series, ch);
        end
    end % for channels avail
    
    
end % for series

%% metadata are created, now write the metadata and the data
% Create ImageWriter
writer = loci.formats.ImageWriter();
writer.setWriteSequentially(true);
writer.setMetadataRetrieve(metadata);
% available compression 'JPEG' 'JPEG-2000' 'JPEG-2000 Lossy' 'LZW' 'Uncompressed' 'zlib'
writer.setCompression('LZW');
writer.getWriter(fname).setBigTiff(true);
writer.setId(fname); 

% fix suggested by Sebastien and Melissa
ifd = loci.formats.tiff.IFD();
disp(ifd.getIFDValue(ifd.ROWS_PER_STRIP));
ifd.putIFDValue(ifd.ROWS_PER_STRIP, szY);
owriter = writer.getWriter(fname);

verbose=0;

%% SERIES 0 [dFLIM_Images]
% define the data conversion
getBytes = @(x) loci.common.DataTools.shortsToBytes(x(:), 0);
owriter.setSeries(0);
index=0;
for z=1:szZ
    for frame=1:nFrames
        for ch=1:nChan
            infostr=['DFI: z=' num2str(z) '/' num2str(szZ) '; ' ...
                'fr=' num2str(frame) '/' num2str(nFrames) '; ' ...
                'dChannel=' num2str(ch) ' [' num2str(ch) '/' num2str(nChan) ']; '];
            
            if verbose, disp([num2str(index) ' ' infostr]); end
            
          
            % first the .img
            owriter.saveBytes(index, getBytes(uint16(dFLIMImageData{3*ch-2,frame}')),ifd); index=index+1;
            
            % then the .nmg
            owriter.saveBytes(index, getBytes(uint16(dFLIMImageData{3*ch-1,frame}')),ifd); index=index+1;
            
            % then the .adjusted tmg
            owriter.saveBytes(index, getBytes(uint16(dFLIMImageData{3*ch-0,frame}')),ifd); index=index+1;
        end
    end
end

%% SERIES 1 [dFLIM_XYTs]
% define the data conversion
getBytes = @(x) loci.common.DataTools.shortsToBytes(x(:), 0);
% owriter.setId([fname0 '_XYT.ome.tif']); % (outputPath);
owriter.setSeries(1);
index=0;
for z=1:szZ
    for ch=1:nChan
        for bin=1:nBins
            infostr=['XYT: z=' num2str(z) '/' num2str(szZ) '; ' ...
                'bin=' num2str(bin) '/' num2str(nBins) '; ' ...
                'dChannel=' num2str(ch) ' [' num2str(ch) '/' num2str(nChan) ']; '];
            
            if verbose, disp([num2str(index) ' ' infostr]); end
            
            % extract the xy plane for this bin
            plane = uint16(dFLIMXYTData{ch}(:,:,bin)); % not bothering to flip xy here
            owriter.saveBytes(index, getBytes(plane(:)),ifd); index=index+1;
        end
    end
end

%% SERIES 2 [dFLIM_Histos]
% define the data conversion
getBytes = @(x) loci.common.DataTools.doublesToBytes(x(:), 0);
% owriter.setId([fname0 '_Histos.ome.tif']); % (outputPath);
owriter.setSeries(2);
index=0;
for z=1:szZ
    for frame=1:nFrames
        for ch=1:nChan
            % get the histo data structure (not shifted!!)
            dfh = dFLIMHistoData{ch,frame};
            
            infostr=['Histo: z=' num2str(z) '/' num2str(szZ) '; ' ...
                'fr=' num2str(frame) '/' num2str(nFrames) '; ' ...
                'dChannel=' num2str(ch) ' [' num2str(ch) '/' num2str(nChan) ']; '];
            
            if verbose, disp([num2str(index) ' ' infostr]); end
            
            % write the "xy plane" for this histo
            owriter.saveBytes(index, getBytes(dfh)); index=index+1;
        end
    end
end

owriter.close();
toc;

end % function [dF_saveDataToOMETiff]