[ImageJ-devel] [fiji-devel] slow opening of tif files using scifio-based ImgOpener

[Melissa Linkert]

Hi Tobias,

> recently I ran across a problem with the scifio-based ImgOpener of ImgLib2.
> I wanted to load stacks from series of tif files which were all in the same directory (about 100.000 of them).
> With ImgOpener, this was imbearably slow, so I decided to load the files using ImageJ1 and wrapping the resulting ImagePluses into imglib2 containers.
> 
> Today, I created a benchmark, that illustrates the problem.
> You can find it here: https://github.com/tpietzsch/TifBenchmark
> It is derived from Johannes' https://github.com/imagej/minimal-ij1-plugin, so you can simply import the maven project in Eclipse and try it out easily.
> 
> The results are disillusioning.
> With just a single tif, scifio opens the file 10x slower than ImageJ1. Bad, but maybe bearable.
> With 100.000 tif files in the same directory, scifio is 400x slower! That is 0.1s for loading 50 tifs from ImageJ vs 55s using scifio!!!
> 
> Can anyone explain this behavior?

Bio-Formats/SCIFIO is known to be slower than ImageJ when opening plain
TIFF files.  See:

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

That ticket (and several other performance improvements in Bio-Formats) are at
the top of my to-do list for the next few weeks.

Regards,
-Melissa

On Wed, Feb 06, 2013 at 01:10:45AM +0100, Tobias Pietzsch wrote:
> Hi,
> 
> recently I ran across a problem with the scifio-based ImgOpener of ImgLib2.
> I wanted to load stacks from series of tif files which were all in the same directory (about 100.000 of them).
> With ImgOpener, this was imbearably slow, so I decided to load the files using ImageJ1 and wrapping the resulting ImagePluses into imglib2 containers.
> 
> Today, I created a benchmark, that illustrates the problem.
> You can find it here: https://github.com/tpietzsch/TifBenchmark
> It is derived from Johannes' https://github.com/imagej/minimal-ij1-plugin, so you can simply import the maven project in Eclipse and try it out easily.
> 
> The results are disillusioning.
> With just a single tif, scifio opens the file 10x slower than ImageJ1. Bad, but maybe bearable.
> With 100.000 tif files in the same directory, scifio is 400x slower! That is 0.1s for loading 50 tifs from ImageJ vs 55s using scifio!!!
> 
> Can anyone explain this behavior?
> This needs to be fixed if we expect anyone to seriously use the ImgOpener…
> 
> best regards,
> Tobias
> 
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