protoTypeSave_OME_TIFF.m

function Save_OME_TIFF(stackList)
% eventually integrate directly into StitchStacks (probably makes more sense)


% Save a 5D matrix into an OME-TIFF using Bio-Formats library
%
% SYNOPSIS bfsave(I, outputPath)
%          bfsave(I, outputPath, dimensionsOrder)
%
% INPUT:
%       I - a 5D matrix containing the pixels data
%
%       outputPath - a string containing the location of the path where to
%       save the resulting OME-TIFF
%
%       dimensionOrder - optional. A string representing the dimension
%       order, Default: XYZCT.
%
% OUTPUT
%

% OME Bio-Formats package for reading and converting biological file formats.
%
% Copyright (C) 2012 - 2013 Open Microscopy Environment:
%   - Board of Regents of the University of Wisconsin-Madison
%   - Glencoe Software, Inc.
%   - University of Dundee
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as
% published by the Free Software Foundation, either version 2 of the
% License, or (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License along
% with this program; if not, write to the Free Software Foundation, Inc.,
% 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

% Check loci-tools jar is in the Java path
%bfCheckJavaPath();

% Not using the inputParser for first argument as it copies data
%assert(isnumeric(I), 'First argument must be numeric');


% List all values of DimensionOrder
dimensionOrderValues = ome.xml.model.enums.DimensionOrder.values();
dimensionsOrders = cell(numel(dimensionOrderValues), 1);
for i = 1 :numel(dimensionOrderValues),
    dimensionsOrders{i} = char(dimensionOrderValues(i).toString());
end

% Input check
%ip = inputParser;
%ip.addRequired('outputPath', @ischar);
%ip.addOptional('dimensionOrder', 'XYZCT', @(x) ismember(x, dimensionsOrders));
%ip.parse(outputPath, varargin{:});

% get first stack and its associated metadata
stackObj = stackList(1);
metaObj = stackObj.metadata;

% Create metadata for ome.tiff output
toInt = @(x) ome.xml.model.primitives.PositiveInteger(java.lang.Integer(x));
metadata = loci.formats.MetadataTools.createOMEXMLMetadata();
metadata.createRoot();
metadata.setImageID(metaObj.seriesName, metaObj.seriesNum);
metadata.setPixelsID(['Pixels:', num2String(metaObj.seriesNum], ...
                     metaObj.seriesNum);
metadata.setPixelsBinDataBigEndian(java.lang.Boolean.TRUE, ...
                                   metaObj.seriesNum, metaObj.seriesNum);

% Set dimension order
dimensionOrderEnumHandler = ome.xml.model.enums.handlers.DimensionOrderEnumHandler();
dimensionOrder = dimensionOrderEnumHandler.getEnumeration(ip.Results.dimensionOrder);
metadata.setPixelsDimensionOrder(dimensionOrder, metaObj.seriesNum);

% Set pixels type
pixelTypeEnumHandler = ome.xml.model.enums.handlers.PixelTypeEnumHandler();
if strcmp(metaObj.intTypeName, 'single')
    pixelsType = pixelTypeEnumHandler.getEnumeration('float');
else
    pixelsType = pixelTypeEnumHandler.getEnumeration(metaObj.intTypeName);
end
metadata.setPixelsType(pixelsType, metaObj.seriesNum);

% Read pixels size from image and set it to the metadat
logical = metaObj.logical;
sizeX = logical(1);
sizeY = logical(2);
sizeZ = logical(3);
sizeC = metaObj.numChannels;
assert(sizeC == length(stackList), ...
       'Number of stacks doesn''t match number of channels')
sizeT = 1;  % assumption for now, was: size(I, find(ip.Results.dimensionOrder == 'T'));
metadata.setPixelsSizeX(toInt(sizeX), metaObj.seriesNum);
metadata.setPixelsSizeY(toInt(sizeY), metaObj.seriesNum);
metadata.setPixelsSizeZ(toInt(sizeZ), metaObj.seriesNum);
metadata.setPixelsSizeC(toInt(sizeC), metaObj.seriesNum);
metadata.setPixelsSizeT(toInt(sizeT), metaObj.seriesNum);

% Set channels ID and samples per pixel
%for i = 1: sizeC
%    metadata.setChannelID(['Channel:0:' num2str(i-1)], 0, i-1);
%    metadata.setChannelSamplesPerPixel(toInt(1), 0, i-1);
%end
metadata.setChannelID(metaObj.channelName, metaObj.seriesNum, ...
                      metaObj.channelNum);
metadata.setChannelSamplesPerPixel(toInt(1), metaObj.seriesNum, ...
                      metaObj.channelNum);



% Here you can edit the function and pass metadata using the adequate set methods, e.g.
physical = metaObj.physical;
metadata.setPixelsPhysicalSizeX(...
  ome.xml.model.primitives.PositiveFloat(java.lang.Double(physical(1))), ...
  metaObj.seriesNum);
metadata.setPixelsPhysicalSizeY(...
  ome.xml.model.primitives.PositiveFloat(java.lang.Double(physical(1))), ...
  metaObj.seriesNum);
metadata.setPixelsPhysicalSizeZ(...
  ome.xml.model.primitives.PositiveFloat(java.lang.Double(physical(1))), ...
  metaObj.seriesNum);
%
% For more information, see http://trac.openmicroscopy.org.uk/ome/wiki/BioFormats-Matlab
%
% For future versions of this function, we plan to support passing metadata as
% parameter/key value pairs

% Create ImageWriter
writer = loci.formats.ImageWriter();
% think about enabling this if I know for sure planes will be written in
% sequential order (z1 -zN for chan1, then chan2 -> chanN for time1, time2, ...
%writer.setWriteSequentially(true);
writer.setMetadataRetrieve(metadata);
outputPath = metaObj.makeOmeTiffName();
writer.setId(outputPath);

% Load conversion tools for saving planes
switch metaObj.intTypeName
    case {'int8', 'uint8'}
        getBytes = @(x) x(:);
    case {'uint16','int16'}
        getBytes = @(x) loci.common.DataTools.shortsToBytes(x(:), 0);
    case {'uint32','int32'}
        getBytes = @(x) loci.common.DataTools.intsToBytes(x(:), 0);
    case {'single'}
        getBytes = @(x) loci.common.DataTools.floatsToBytes(x(:), 0);
    case 'double'
        getBytes = @(x) loci.common.DataTools.doublesToBytes(x(:), 0);
end

% Save planes to the writer
indexOffset = sizeZ * (metaObj.channelNum + metaObj.time * sizeC) - 1;
for z = 1 : sizeZ
    index = z + indexOffset;

    %[i, j, k] = ind2sub([size(I, 3) size(I, 4) size(I, 5)],index);
    %plane = I(:, :, i, j, k)';
    %writer.saveBytes(index - 1, getBytes(plane));
    write.saveBytes(index, stackObj.getSliceZ(z));
end
writer.close();

end