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 > > -- > -- > Please avoid top-posting, and please make sure to reply-to-all! > > Mailing list web interface: http://groups.google.com/group/fiji-devel > > --- > You received this message because you are subscribed to the Google Groups > "Fiji-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > For more options, visit https://groups.google.com/groups/opt_out. > > _______________________________________________ ImageJ-devel mailing list [email protected] http://imagej.net/mailman/listinfo/imagej-devel
