Hi Melissa, That is awesome! Thanks a lot for tackling these problems.
Out of curiosity, could you briefly explain (if there is an easy explanation) why the 100.000-files-issue happens? Is bioformats analyzing the directory the TIFF file lives in? Is there a way to turn this off? best regards, Tobias On Feb 6, 2013, at 3:08 AM, Melissa Linkert wrote: > 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
