[ome-devel] tif import performance

[Macura, Tomasz (NIH/NIA/IRP)]

Dear Richard,

Tiff tag reading is indeed a bottleneck. I am not sure what you mean by
perl->libtiff, but our tiff tag reading library is 
OME/src/perl2/OME/ImportEngine/TIFFUtils.pm .

Reading tiff tags amounts to doing many reads (readData() calls) on the
original file. Each call to readData() is much
less efficient then ideal because readData() has to get the data from OMEIS
(using the OMEIS method ReadFile()
 http://www.openmicroscopy.org/api/omeis/files.html#ReadFile) and there is a
lot of surrounding logic written in Perl 
that deals with caching. As you can see, due to our requirements with regard
to OMEIS we can't use Perl's built-in libraries.

The end result is that the TIFF perl command readTiffIFD() takes alot
(10-100 times) longer than the libtiff's tifffinfo CLI program.

The optimizations I did with regard to improving tiff tag reading was (1)
TIFF caching and (2) increased IFD specificity. So right
now the tags have to be read only once and its possible to specify quite
explicitly which tags are required. This means that as
few as possible readTiffIFD() calls are made per image.

In my limited imagination, the only way of improving performance is to get
OMEIS (which is written in C) to use libtiff to
get the TIFF tags and send them over, in mass, to the ImportEngine.
Implementing this is surely very feasible but I am not able to
comment on the larger issues (e.g. OMEIS feature creep).

Regards,

Tom