[ome-devel] TIFF pyramid support in Bio-Formats - reference files for review

[Damir Sudar]

Hi Roger,

On 3/23/2018 2:46, Roger Leigh wrote:
> On 23/03/18 01:40, Damir Sudar wrote:
>> TIFFWriteDirectoryTagSubifd: Illegal value for SubIFD tag.
>> TIFFWriteDirectoryTagSubifd: Illegal value for SubIFD tag.
>> I'm using libtiff 4.0.9 and its associated tools on Ubuntu 14.04. The
>> error does not happen with the scn files provided. Could it be related
>> to having an offset value that is too large for a non-BigTIFF file?
> Yes, you need to apply this change to libtiff:
>   https://gitlab.com/libtiff/libtiff/merge_requests/25/diffs
> Hopefully this will be in libtiff 4.0.10.  We must be the first users of
> tiffset with BigTIFF images to run into this problem.
>
Indeed, with your merge request applied, it works correctly for svs 
files and almost for my ptifs. I'm still chasing a small bug around line 
133 that causes the subresolutions pyramid to appear in its own 
top-level IFD instead of all being stuck as SubIFDs into the single 
top-level IFD. I'll keep chasing but in case you see my mistake?

> I should also mention that the scripts have only been tested on Linux,
> and might not run on other systems.  Hopefully they will be short-lived;
> as soon as we have bfconvert supporting pyramids they can be forgotten.

Yes, but for their intended purpose, these scripts are great.
Once I get the ptif one to work correctly, I'll mock up some more 
example files including some with larger numbers of channels, Z and t.

> - also, all these examples carry some of those ancillary images such as
>> slide labels, overview images, etc. While the scripts handled those
>> correctly as far as I can see, a reader would have to be pretty smart to
>> figure out which of the contents of such an output file is the actual
>> image and which are those ancillary images.
>
> Absolutely.  We will need to do something about these as a followup
> task, to add the metadata to identify these as labels, overviews, etc.
>
Ok, I'll start looking at options how to do so.

Cheers,
- Damir
>
> Kind regards,
> Roger
>
> The University of Dundee is a registered Scottish Charity, No: SC015096

-- 
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
http://biosciences.lbl.gov/profiles/damir-sudar-2/

Visiting Scientist, Oregon Health & Science University