[ome-users] Invalid values stored in TIFF-tag 'StripByteCounts' when writing striped OME-TIFF

[Roger Leigh]

On 07/09/2012 16:31, Matthias Baldauf wrote:
> I am using the Bio-Formats Java library (trunk build) to write an
> OME-TIFF sequentially strip per strip.
> It is basically the same approach I mentioned in a previous post
> (http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-August/003178.html),
> but now I am reading the JPEG in stripes and store them strip per strip
> in an OME-TIFF. It works great for striped uncompressed OME-TIFFs.
>
> However, when using LZW compression, it nearly ever results in an
> OME-TIFF which cannot be opened.
> To locate the error I analyzed the IFD of the TIFF and observed that the
> tag 'StripByteCounts' doesn’t contain valid values.
> In the case when there are just a few stripes in the OME-TIFF, the
> values of 'StripByteCounts' are too large, even exceeding the number of
> bytes when the strip would be uncompressed.
> In the case when there are more stripes in the OME-TIFF, the values of
> 'StripByteCounts' are zero.
> So I had a look at the IFD-class in the loci.formats.tiff package an
> encountered the following lines in the getStripByteCounts() method:
>
>      if (getCompression() == TiffCompression.LZW) {
>        for (int i=0; i<byteCounts.length; i++) {
>          counts[i] = byteCounts[i] * 2;
>        }
>      }
>
> I removed the multiplication (* 2) and it seems to solve the error with
> the wrong values of 'StripByteCounts'.
> The OME-TIFFs can be opened now (even containing many stripes).
> The multiplication increases the values of 'StripByteCounts' every time
> a strip gets stored in the OME-TIFF.
> This would explain the very large numbers and, when more strips are
> added, the zeros because of an overflow.

Just to add a small additional bit of data:

This logic was added to getStripByteCounts() in commit 0599079, but for
all compressed formats, and was switched to LZW-only as above in
bf1dcbe9.  I'm not sure what makes LZW special here compared with the
other compression formats.


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096