function dF_saveAsOMETiff(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)
%
% Gary Yellen 2014-10-31
%% OME PEOPLE: THIS FILE IS INCLUDED ONLY AS AN EXAMPLE OF USING THE
%    OMETiffWriter class.  It requires data classes that are particular
%    to our lab, but hopefully will help you see both the standard and 
%    non-standard uses of the OMETiffWriter.
%%

global state savedHeaderString

% DEBUG OPTIONS
useAnnotations=1;
useDatasets=1 && useAnnotations;
useIRFAnnotations=0 && useAnnotations;
usePlaneDeltaAnnotation=1;


%% give the user a chance to set the save name
fileName='';
[fname, path]=uiputfile('*.ome.tif','Save data to OME-Tiff as...',fileName);
fname=[path fname];
fname0=fname(1:end-8); % without the extension

% use the OMETiffWriter_gy object for writing
OTW = OMETiffWriter_gy(fname,'FluorescenceLifetime','Peredox in DGN with stimulation');

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

% number of Z slices
if numel(sz)<3
    szZ=1;
else
    szZ=sz(3);
end

% number of dFLIM channels
used = arrayfun(@(x) x.nPixels~=0, dFLIMImageData);
nChan = sum(used(:,1,1));
channelsAvail = find(arrayfun(@(x) ~isempty(x.img), dFLIMImageData(:,1,1))');

% size of images
typicalIndex = find(used,1,'first');
typicalDFI=dFLIMImageData(typicalIndex);
szX = typicalDFI.nPixels;
szY = typicalDFI.nLines;
nFrames = sz(2);

% histo info
nBins = numel(dFLIMHistoData(typicalIndex).Data);

% XYT available?
xytAvail = ~isempty(dFLIMXYTData) && ~isempty(dFLIMXYTData(channelsAvail(1),1).Data);
tic;

%% Create metadata
stateVal = @(x) valueFromHeaderString(x,savedHeaderString);
toInt = @(x) ome.xml.model.primitives.PositiveInteger(java.lang.Integer(x));
toNNInt = @(x) ome.xml.model.primitives.NonNegativeInteger(java.lang.Integer(x));




%% experiment annotation

if useAnnotations
    expt=state.exptNotes;
    % --- Comment annotations
    OTW.addImageAnnotation('Comment','Genotype',expt.prep.genotype);
    OTW.addImageAnnotation('Comment','Gender',expt.prep.gender);
    OTW.addImageAnnotation('Comment','Fluor1',expt.prep.fluor1);
    OTW.addImageAnnotation('Comment','Vector1',expt.prep.vector1);
    OTW.addImageAnnotation('Comment','Fluor1Note',expt.prep.vectorNote1);
    OTW.addImageAnnotation('Comment','Fluor2',expt.prep.fluor2);
    OTW.addImageAnnotation('Comment','Vector2',expt.prep.vector2);
    OTW.addImageAnnotation('Comment','Fluor2Note',expt.prep.vectorNote2);
    OTW.addImageAnnotation('Comment','Fluor3',expt.prep.fluor3);
    OTW.addImageAnnotation('Comment','Vector3',expt.prep.vector3);
    OTW.addImageAnnotation('Comment','Fluor3Note',expt.prep.vectorNote3);
    OTW.addImageAnnotation('Comment','InjectionSite',expt.prep.injectionSite);
    OTW.addImageAnnotation('Comment','Surgery',expt.prep.surgery);
    OTW.addImageAnnotation('Comment','SliceNotes',expt.prep.sliceNotes);
    OTW.addImageAnnotation('Comment','PerfusionEvents',toString(expt.perfusion.events));
    OTW.addImageAnnotation('Comment','Anesthesia',toString(expt.anesthesia.events));
    psetname=stateVal('state.pulses.pulseSetName');
    if ~isempty(psetname)
        OTW.addImageAnnotation('Comment','PulseSetName',psetname);
    end
    
    % --- Timestamp annotations
    OTW.addImageAnnotation('Timestamp','SliceTime',expt.prep.sliceTime);

    % --- Double Annotations
    % first the non-channel Double-valued annotations
    OTW.addImageAnnotation('Double','AgeNow',expt.prep.ageNow);
    OTW.addImageAnnotation('Double','AgeInj',expt.prep.ageInj);
    if ~isempty(stateVal('state.motor.absXPosition'))
        spos={'absX' 'absY' 'absZ' 'relX' 'relY' 'relZ'} ;
        for k=1:numel(spos)
            posval = stateVal(['state.motor.' spos{k} 'Position']);
            OTW.addImageAnnotation('Double',['Position:' spos{k}],posval);
        end
    end
    for k=1:6 % possible lineMonitor settings
        lmname = stateVal(['state.lm.paramName' num2str(k)]);
        if ~isempty(lmname)
            lmvalue = stateVal(['state.lm.paramValue' num2str(k)]);
            OTW.addImageAnnotation('Double',['LM:' lmname],lmvalue); 
        end
    end
    cycpos = stateVal('state.cycle.currentCyclePosition');
    if ~isempty(cycpos)
        OTW.addImageAnnotation('Double','CyclePosition',cycpos);
    end
    zspace = stateVal('state.acq.zStepSize');
    if ~isempty(zspace)
        OTW.addImageAnnotation('Double','Z-Spacing',zspace); 
    end
    
    % now set the TPeakIRF annotations for each included channel
    if useIRFAnnotations
        % TODO get these from the DFI object?
        tPeakIRFannot=zeros(8,1);
        for ch=channelsAvail
            chID = num2str(ch,'%02i');
            idx = OTW.addAnnotation('Double',['TPeakIRF:Ch' chID],state.dFLIM.dChannels{ch}.tPeakIRF);
            tPeakIRFannot(ch)=idx;
        end
    end % if useIRFAnnotations
    
    % --- Boolean Annotations
    tf=stateVal('state.acq.lineScan'); if ~isempty(tf), tf=0; end
    OTW.addImageAnnotation('Boolean','Linescan[X vs T]',tf);
    
    tf=stateVal('state.acq.bidi'); if ~isempty(tf), tf=0; end
    OTW.addImageAnnotation('Boolean','BidirectionalScan',tf);

    % XML annotation
    OTW.addImageAnnotation('XML','exptNotes', makeXML('exptNotes',state.exptNotes, ...
        {'dichroics','emfilters','objectives','gh','genotypes','perfusionEvents','anesthesiaEvents','fluors','vectors','configGlobals','globalGUIPairs'} ...
        ));

end % if useAnnotations
%% instrument and experiment metadata
OTW.metadata.setInstrumentID('Instrument:0',0);
OTW.metadata.setMicroscopeManufacturer('Thorlabs',0);
OTW.metadata.setMicroscopeModel(state.exptNotes.optics.instrument,0);
OTW.metadata.setObjectiveID('Objective:0',0,0)
OTW.metadata.setObjectiveModel(state.exptNotes.optics.objective,0,0);
OTW.metadata.setObjectiveNominalMagnification(java.lang.Double(state.exptNotes.optics.mag),0,0);

idxFilter=0;
channelFilter(1:8)=-1;
for chan=channelsAvail
    ch = 1+mod(chan-1,4);
    if channelFilter(ch)>=0 % already assigned
        channelFilter(chan)=channelFilter(ch);
    else
        OTW.metadata.setFilterID(['Filter:' num2str(ch)],0,idxFilter);
        OTW.metadata.setFilterModel(state.exptNotes.channels{ch}.em,0,idxFilter);
        OTW.metadata.setDichroicID(['Dichroic:' num2str(ch)],0,idxFilter);
        OTW.metadata.setDichroicModel(state.exptNotes.channels{ch}.dc,0,idxFilter);
        channelFilter(chan)=idxFilter;
        idxFilter = idxFilter+1;
    end
end
%% create the Dataset references
if useDatasets
    OTW.metadata.setDatasetID('Dataset:All',0);
    OTW.metadata.setDatasetName('BigExperimentToday',0);
    OTW.metadata.setDatasetID('Dataset:dfi',1);
    OTW.metadata.setDatasetName('BigExperimentToday_DFI',1);
    OTW.metadata.setDatasetID('Dataset:xyt',2);
    OTW.metadata.setDatasetName('BigExperimentToday_XYT',2);
    OTW.metadata.setDatasetID('Dataset:dfh',3);
    OTW.metadata.setDatasetName('BigExperimentToday_DFH',3);
end
%% create the metadata for each series
for series=0:2
    sSeries = num2str(series);
    % a modest provision for cases where acqTime does not include the date.
    acqdate=state.dFLIM.acqTime;
    if isempty(strfind(acqdate,'201')) % no year included
        datepos=strfind(state.dFLIM.filename,'_201');
        if ~isempty(datepos)
            % try using the last instance
            acqdate2=state.dFLIM.filename(datepos(end)+1:datepos(end)+8);
            acqdate2=[acqdate2(1:4) '-' acqdate2(5:6) '-' acqdate2(7:8) ' ' acqdate];
            try
                datenum(acqdate2);
                acqdate=acqdate2;
            catch
                disp('Warning: Could not infer AcquisitionDate from filename');
            end
        else
            disp('Warning: Could not infer AcquisitionDate from filename');
        end
    end
    
    % Set pixels type
    
    if usePlaneDeltaAnnotation && series~=1
        msPerLine = stateVal('state.acq.msPerLine');
        if isempty(msPerLine), msPerLine = 2.080; end
        frameDeltaT = szY * msPerLine/1000;
    else
        frameDeltaT = 0;
    end
    
    switch series
        case 0  % dFLIMImages
            szXYZCT = [szX szY szZ 3*nChan nFrames];
            imageDescription = ['dFLIM_Images from ' state.dFLIM.filename];
            OTW.defineSeries(acqdate, imageDescription, 'XYCTZ', szXYZCT, 'uint16', frameDeltaT);
            OTW.metadata.setImageInstrumentRef('Instrument:0',series);
            if useDatasets
                OTW.metadata.setDatasetImageRef(['Image:' sSeries],0,series);
                OTW.metadata.setDatasetImageRef(['Image:' sSeries],1,series);
            end
        case 1  % XYT
            if xytAvail
                szXYZCT = [szX szY szZ nChan nBins];
            else
                szXYZCT = [0 0 0 0 0];
            end
            %OMEXMLService.addModuloAlong(md, coreMetadata, series); %
            % interferes with LightPath in 2nd and 3rd series
            imageDescription = ['dFLIM_XYTs from ' state.dFLIM.filename];
            OTW.defineSeries(acqdate, imageDescription, 'XYTCZ', szXYZCT, 'uint16', frameDeltaT);
            OTW.metadata.setImageInstrumentRef('Instrument:0',series);
            if useDatasets
                OTW.metadata.setDatasetImageRef(['Image:' sSeries],0,series);
                OTW.metadata.setDatasetImageRef(['Image:' sSeries],2,series);
            end
        case 2 % Histos
            szXYZCT = [nBins 1 szZ nChan nFrames];
            imageDescription = ['dFLIM_Histos from ' state.dFLIM.filename];
            OTW.defineSeries(acqdate, imageDescription, 'XYCTZ', szXYZCT, 'double', frameDeltaT);
            OTW.metadata.setImageInstrumentRef('Instrument:0',series);
            if useDatasets
                OTW.metadata.setDatasetImageRef(['Image:' sSeries],0,series);
                OTW.metadata.setDatasetImageRef(['Image:' sSeries],3,series);
            end
    end % switch series (size assignment)
   
    % Set channels ID and samples per pixel
    suffix={':img' ':nmg' ':tmg'};
    
    for i = 1:numel(channelsAvail)
        chan = channelsAvail(i);
        chID = num2str(chan,'%02i');
        laserChoice = num2str(1 + floor(chan/5));
        if (series)==0
            for j=1:3
                ch = (i-1)*3+j-1;
                chname = ['dChannel:' chID suffix{j}];
                OTW.defineChannel(chname, series, ch);
                % next line intended to be setChannelAnnotationRef (but it doesn't work properly)
                if useIRFAnnotations, OTW.metadata.setChannelAnnotationRef(OTW.metadata.getDoubleAnnotationID(tPeakIRFannot(chan)),series,ch,tPeakIRFannot(chan)); end
                
                OTW.metadata.setLightPathEmissionFilterRef(['Filter:' num2str(1+mod(chan-1,4))],series,ch,channelFilter(chan));
                OTW.metadata.setLightPathDichroicRef(['Dichroic:' num2str(1+mod(chan-1,4))],series,ch);
                OTW.metadata.setChannelExcitationWavelength(toInt(state.exptNotes.optics.(['laser' laserChoice])),series,ch);
                pcellsetting = stateVal(['state.pcell.pcellScanning' laserChoice]);
                if ~isempty(pcellsetting)
                    OTW.metadata.setChannelPockelCellSetting(java.lang.Integer(100*pcellsetting),series,ch);
                end
            end
        else
            ch = (i-1);
            chname = ['dChannel:' chID ];
            OTW.defineChannel(chname, series, ch);
            % next line intended to be setChannelAnnotationRef (but it doesn't work properly)
            if useIRFAnnotations, OTW.metadata.setChannelAnnotationRef(OTW.metadata.getDoubleAnnotationID(tPeakIRFannot(chan)),series,ch,tPeakIRFannot(chan)); end
            OTW.metadata.setLightPathDichroicRef(['Dichroic:' num2str(1+mod(chan-1,4))],series,ch);
            OTW.metadata.setLightPathEmissionFilterRef(['Filter:' num2str(1+mod(chan-1,4))],series,ch,channelFilter(chan));
            OTW.metadata.setChannelExcitationWavelength(toInt(state.exptNotes.optics.(['laser' laserChoice])),series,ch);
            pcellsetting = stateVal(['state.pcell.pcellScanning' laserChoice]);
            if ~isempty(pcellsetting)
                OTW.metadata.setChannelPockelCellSetting(java.lang.Integer(100*pcellsetting),series,ch);
            end
        end
        
    end % for channels avail
    
end % for series

% add the ModuloAlongT annotation to series 1
OTW.finalizeImageAnnotations();

% have to do this last!  can't add annotations after this
OTW.defineModuloAlongT(1 , 0, state.dFLIM.nsPerPoint, 255*state.dFLIM.nsPerPoint);

OTW.finalizeMetadata();


%% metadata are created, now write the metadata and the data

    verbose=0;
    
    %% SERIES 0 [dFLIM_Images]
    % define the data conversion
    index=0;
    for z=1:szZ
        for frame=1:nFrames
            for ch=channelsAvail
                if verbose
                    infostr=['DFI: z=' num2str(z) '/' num2str(szZ) '; ' ...
                        'fr=' num2str(frame) '/' num2str(nFrames) '; ' ...
                        'dChannel=' num2str(ch) ' [' num2str(find(ch==channelsAvail)) '/' num2str(nChan) ']; '];
                    disp([num2str(index) ' ' infostr]);
                end
                
                % get the data
                dfi = dFLIMImageData(ch,frame,z);
                
                OTW.writePlane(uint16(dfi.img),index==0);
                OTW.writePlane(uint16(dfi.nmg));
                OTW.writePlane(uint16(dfi.tmg));

                index = index + 3;
            end
        end
    end
    
    %% SERIES 1 [dFLIM_XYTs]
    index=0;
    for z=1:szZ
        for ch=channelsAvail
            % get the xyt data structure (not shifted!!)
            dfxyt = dFLIMXYTData(ch,1,z).Data;
            dfxyt = permute(dfxyt,[2 3 1]); % this structure is ordered y/x/bin
            
            for bin=1:nBins
                if verbose
                    infostr=['XYT: z=' num2str(z) '/' num2str(szZ) '; ' ...
                        'bin=' num2str(bin) '/' num2str(nBins) '; ' ...
                        'dChannel=' num2str(ch) ' [' num2str(find(ch==channelsAvail)) '/' num2str(nChan) ']; '];
                    disp([num2str(index) ' ' infostr]);
                end
                
                OTW.writePlane(dfxyt(:,:,bin),index==0);
                index=index+1;
            end
        end
    end
    
    %% SERIES 2 [dFLIM_Histos]
    index=0;
    for z=1:szZ
        for frame=1:nFrames
            for ch=channelsAvail
                % get the histo data structure (not shifted!!)
                dfh = dFLIMHistoData(ch,frame,z);

                if verbose
                    infostr=['Histo: z=' num2str(z) '/' num2str(szZ) '; ' ...
                        'fr=' num2str(frame) '/' num2str(nFrames) '; ' ...
                        'dChannel=' num2str(ch) ' [' num2str(find(ch==channelsAvail)) '/' num2str(nChan) ']; '];
                    disp([num2str(index) ' ' infostr]);
                end
                
                OTW.writePlane(dfh.Data(:)',index==0);
                index=index+1;

            end
        end
    end
    
    OTW.close;
    toc;
    


end % function [dF_saveDataToOMETiff]

function str = toString(cellStrings)
str='';
for k=1:numel(cellStrings)
    str = [str cellStrings{k}];
    if k<numel(cellStrings)
        str = [str '||'];
    end
end
end