Hi Melissa,<div><br></div><div>> There is already a ticket for this:<br><br>Great! And sorry for forgetting about it. I think the benchmark is a great way to validate progress on that ticket, too.</div><div><br></div><div>
Regards,</div><div>Curtis</div><div><br><br><div class="gmail_quote">On Thu, Nov 1, 2012 at 2:54 PM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Curtis,<br>
<div class="im"><br>
> Johannes & I were discussing how the speed of the Bio-Formats TIFF reader<br>
> could be improved in common cases. Two main ideas:<br>
<br>
</div>There is already a ticket for this:<br>
<br>
<a href="http://trac.openmicroscopy.org.uk/ome/ticket/9228" target="_blank">http://trac.openmicroscopy.org.uk/ome/ticket/9228</a><br>
<br>
You and Johannes were both CC'd when that ticket was created.<br>
I have updated the ticket to reference this thread.<br>
<br>
Regards,<br>
-Melissa<br>
<div><div class="h5"><br>
On Thu, Nov 01, 2012 at 01:39:54PM -0500, Curtis Rueden wrote:<br>
> Hi all,<br>
><br>
> Johannes & I were discussing how the speed of the Bio-Formats TIFF reader<br>
> could be improved in common cases. Two main ideas:<br>
><br>
> 1) If the data was written by either ImageJ or Bio-Formats (either which<br>
> can be detected by examining the first IFD), we could make assumptions<br>
> about the structure of the pixel data. ImageJ itself does this when reading<br>
> TIFF files (assumes planes are written in contiguous order) which allows it<br>
> to read in TIFFs very quickly. Unfortunately, ImageJ fails to handle TIFFs<br>
> that do not meet these assumptions. But Bio-Formats could fall back to its<br>
> more general parsing logic.<br>
><br>
> 2) Parse IFDs only lazily per plane as each plane is requested, rather than<br>
> fully populating them all up front. AFAIK, the first IFD is really the only<br>
> important one for detecting whether a file should be classified as a<br>
> particular subtype of TIFF. Also AFAIK, we would still need to walk the IFD<br>
> linked list just to count the total number of image planes (unless we could<br>
> obtain that information in some other format-specific way), but it would<br>
> probably be faster than parsing all IFDs fully up-front.<br>
><br>
> We think that Bio-Formats could deliver the best of both worlds<br>
> (correctness and performance), if we added some heuristics along these<br>
> lines in common cases. It could make a big difference in usability.<br>
><br>
> Do other Bio-Formats devs agree? If so, I can file a ticket on the OME Trac<br>
> for it, if one doesn't already exist.<br>
><br>
> Regards,<br>
> Curtis<br>
<br>
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</blockquote></div><br></div>