https://github.com/QBioLab/CountmRNA.jl
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Tip revision: 27fa41066bf09a3c1ca00fd333f72755e481b16f authored by H.F on 13 April 2021, 10:57 UTC
upload running script
Tip revision: 27fa410
tiffxml.jl
using LightXML
"""
Verision Comment
v0.1     hf, firstversion
v0.2     hf, use exiftool instead of tiffcommit

ref: http://web.mit.edu/jhawk/mnt/cgs/Image-ExifTool-6.99/html/exiftool_pod.html
    https://exiftool.org/TagNames/EXIF.html
    https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/specification.html
    https://micro-manager.org/wiki/Micro-Manager_File_Formats
"""

"""
Create and return XML string with xyzt
"""
function generatexml(SizeX::Integer, SizeY::Integer, SizeZ::Integer, SizeT::Integer)
    tiffXML = XMLDocument();
    OME = create_root(tiffXML, "OME");
    xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" 
    xmlns_xsi="http://www.w3.org/2001/XMLSchema-instance"
    Creator="OME Bio-Formats 5.2.2" 
    UUID="urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629" # use fixed value now
    xsi_schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"
    OME_attributes = Dict("xmlns"=>xmlns, "xmlns:xsi"=>xmlns_xsi, "Creator"=>Creator, "UUID"=>UUID, "xsi:schemaLocation"=>xsi_schemaLocation)
    set_attributes(OME, OME_attributes)
    
    name = "test.tiff"
    Image= new_child(OME, "Image")
    set_attributes(Image, Dict("ID"=>"Image:0", "Name"=>name))
    
    Pixels = new_child(Image, "Pixels");
    SizeC=1; 
    #SizeT=10;  #SizeX=1300; #SizeY=1900; #SizeZ=2;
    PhysicalSizeX=PhysicalSizeY=0.108; PhysicalSizeZ=0.5;
    TimeIncrement=600;
    Pixels_attributes = Dict("ID"=>"Pixels:0","Type"=>"uint16", "BigEndian"=>"false",
    "DimensionOrder"=>"XYZCT", "SizeC"=>1,"SizeX"=>SizeX, "SizeY"=>SizeY, "SizeZ"=>SizeZ, "SizeT"=>SizeT,
    "PhysicalSizeX"=>PhysicalSizeX, "PhysicalSizeY"=>PhysicalSizeY, "PhysicalSizeZ"=>PhysicalSizeZ,
    "PhysicalSizeXUnit"=>"µm", "PhysicalSizeYUnit"=>"µm", "PhysicalSizeZUnit"=>"µm",
    "TimeIncrement"=>TimeIncrement, "TimeIncrementUnit"=>"s");
    set_attributes(Pixels, Pixels_attributes)
    
    Channel_ = new_child(Pixels, "Channel");
    set_attributes(Channel_, Dict("ID"=>"Channel:0:0", "SamplesPerPixel"=>"1"));
    LightPath =new_child(Channel_, "LightPath");
    
    for i in 1:SizeC*SizeZ*SizeT
        new_child(Pixels, "TiffData")
    end
	"""
	for c in 0:SizeC-1
    	for t in 0:SizeT-1
        	for z in 0:SizeZ-1
               TiffData = new_child(Pixels, "TiffData")
               TiffData_attributes = Dict("FirstC"=>c, "FirstT"=>t, "FirstZ"=>z, 
										  "IFD"=>t*SizeZ+z,"PlaneCount"=>1)
                set_attributes(TiffData, TiffData_attributes)
            end
        end
    end
	"""
    tiffXML;
end

"""
Embed OME-XML to tiff with XYZT informance
"""
function embedxml(SizeX::Integer, SizeY::Integer, SizeZ::Integer, SizeT::Integer, img_name::String)
    tiffxml = generatexml(SizeX, SizeY, SizeZ, SizeT);
    print("Embedding OME-XML")
    #run(`/home/hf/Bin/bftools/tiffcomment -set $tiffxml $img_name`);
    if Sys.which("exiftool") == Nothing
        print("Please install exiftool")
    else
		run(`exiftool -ImageDescription=$tiffxml $img_name -overwrite_original`, wait=false)
		#run(pipeline(`echo $tiffxml`, `exiftool -ImageDescription\<= $img_name -overwrite_original`), wait=false)
		#run(`ulimit -s 65536 ; exiftool -ImageDescription\<= $img_name -overwrite_original`, wait=true)
		# run in backgroud to continue next computing work
        # I assume that run computing takes more time to embed xml
        #run(`rm $img_name"_original"`)
    end
    println("")
    nothing;
end
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