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

Tobias Pietzsch pietzsch at mpi-cbg.de
Tue Feb 5 18:10:45 CST 2013


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,

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