[ome-devel] Speeding up the TIFF reader in common cases

[Melissa Linkert]

Hi Curtis,

> Johannes & I were discussing how the speed of the Bio-Formats TIFF reader
> could be improved in common cases. Two main ideas:

There is already a ticket for this:

http://trac.openmicroscopy.org.uk/ome/ticket/9228

You and Johannes were both CC'd when that ticket was created.
I have updated the ticket to reference this thread.

Regards,
-Melissa

On Thu, Nov 01, 2012 at 01:39:54PM -0500, Curtis Rueden wrote:
> Hi all,
> 
> Johannes & I were discussing how the speed of the Bio-Formats TIFF reader
> could be improved in common cases. Two main ideas:
> 
> 1) If the data was written by either ImageJ or Bio-Formats (either which
> can be detected by examining the first IFD), we could make assumptions
> about the structure of the pixel data. ImageJ itself does this when reading
> TIFF files (assumes planes are written in contiguous order) which allows it
> to read in TIFFs very quickly. Unfortunately, ImageJ fails to handle TIFFs
> that do not meet these assumptions. But Bio-Formats could fall back to its
> more general parsing logic.
> 
> 2) Parse IFDs only lazily per plane as each plane is requested, rather than
> fully populating them all up front. AFAIK, the first IFD is really the only
> important one for detecting whether a file should be classified as a
> particular subtype of TIFF. Also AFAIK, we would still need to walk the IFD
> linked list just to count the total number of image planes (unless we could
> obtain that information in some other format-specific way), but it would
> probably be faster than parsing all IFDs fully up-front.
> 
> We think that Bio-Formats could deliver the best of both worlds
> (correctness and performance), if we added some heuristics along these
> lines in common cases. It could make a big difference in usability.
> 
> Do other Bio-Formats devs agree? If so, I can file a ticket on the OME Trac
> for it, if one doesn't already exist.
> 
> Regards,
> Curtis

> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel