Tiff is saved with uncompleted tag content

[JiangXL]

Hi, I try to write below omexml to TiffImages.IMAGEDESCRIPTION tag and save tiff, but saved tiff's IMAGEDESCRIPTION tag always lose final 2 chars! It is so weird... For example, if the original is ...</OME>\n, saved tiff will be ...</OME(julia take \n as a char ). But the dump xml from OMETIFF.jl and simple strings don't show this issue. As the same time, exiftool write tag normally.

run(`exiftool -ImageDescription=$tiffxml $img_name -overwrite_original`

The final goal is to save OMETIFF. To do that, I have to add two more chars in original xml: ...</OME>\n => ...</OME>\n>\n. It will be convenient and excited to write OMETIFF, so I'm looking for your idea.

"<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<OME xsi:schemaLocation=\"http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd\" UUID=\"urn:uuid:39163ae6-e2d4-4bd4-b45f-e29234238f3f\" Creato" ⋯ 579 bytes ⋯ "  </Channel>\n      <TiffData FirstT=\"0\" IFD=\"0\" FirstC=\"0\" PlaneCount=\"1\" FirstZ=\"0\">\n        <UUID FileName=\"4D-series.ome.tif\">urn:uuid:39163ae6-e2d4-4bd4-b45f-e29234238f3f</UUID>\n      </TiffData>\n    </Pixels>\n  </Image>\n</OME>\n"

[tlnagy]

This is definitely a bug. My best guess is that somehow the length of the string is being computed incorrectly?

[tlnagy]

So after digging into this a bit more, it looks like this is caused by the UTF-8 encoding of the OME-XML.

julia> using TiffImages

julia> tf = TiffImages.TiffFile(UInt32);

julia> tag = TiffImages.Tag(TiffImages.IMAGEDESCRIPTION, "αβγ") # extended characters
Tag(IMAGEDESCRIPTION, "αβγ")

julia> write(tf, tag) # this should be false, because extended chars take up more space
true

julia> seekstart(tf.io);

julia> read(tf, TiffImages.Tag) # the last character is missing!
Tag(IMAGEDESCRIPTION, "αβ")

julia> sizeof(tag) # this would be correct if characters were ascii
4

julia> sizeof(tag.data) # what the actual length is
6

The TIFF standard was written prior to UTF-8 so it doesn't seem like there's a standardized way to handle this. But given that Julia uses UTF-8 basically everywhere, we should do our best to encode it properly.

[tlnagy]

This should be fixed by #78, could you please test the latest dev version and see if that fixed your problem?

Also, if you are working on a writer for OME-TIFF files, it would be fantastic if you could submit a PR over at OMETIFF.jl! I've been meaning to do that forever, and would very happy to review it.

EDIT: For at least three years 😅 tlnagy/OMETIFF.jl#30

[JiangXL]

Thanks, I'm working at adapting this code to generate omexml. Although this implementation is only subset of OMEXML, I think it may be very helpful to manage multi dimensions image.