Hi Curtis, Ok, I tried the things you suggested as well as the setGroupFiles( false ) suggested by Lee. Here are the results:
baseline (unmodified ImgOpener): loading 50 tif images using ImageJ, 10000 other tif files in same directory median: 141 ms loading 50 tif images using ImgOpener, 10000 other tif files in same directory median: 6953 ms with setAllowOpenFiles( false ): loading 50 tif images using ImgOpener, 10000 other tif files in same directory median: 5972 ms with setGroupFiles( false ): loading 50 tif images using ImgOpener, 10000 other tif files in same directory median: 2331 ms with both, setAllowOpenFiles( false ) and setGroupFiles( false ): loading 50 tif images using ImgOpener, 10000 other tif files in same directory median: 1070 ms with TiffReader: loading 50 tif images using ImgOpener, 10000 other tif files in same directory median: 5061 ms with TiffReader and setGroupFiles( false ): loading 50 tif images using ImgOpener, 10000 other tif files in same directory median: 568 ms For comparison, the case where there are no other files in the directory baseline (unmodified ImgOpener): loading 50 tif images using ImageJ, 0 other tif files in same directory median: 140 ms loading 50 tif images using ImgOpener, 0 other tif files in same directory median: 1804 ms with TiffReader and setGroupFiles( false ): loading 50 tif images using ImgOpener, 0 other tif files in same directory median: 552 ms That's still 4x slower than ImageJ1 but already getting a lot closer. Nice! best regards, Tobias On Feb 6, 2013, at 6:35 PM, Curtis Rueden wrote: > Hi all, > > > Is there a way to turn this off? > > Yes, you can call imageOpener.setAllowOpenFiles(false) which will prevent > Bio-Formats from doing any directory listings or opening up any files for the > purposes of determining the file format. However, if you set this flag, some > file formats will be improperly identified. > > Out of curiosity: how much does the benchmark improve if that flag is set > inside ImgOpener's createReader method? Another thing you could test, to > determine the performance impact, is to change "new ImageReader" to "new > TiffReader", which explicitly tells ImgOpener to assume everything is a TIFF. > > If such changes vastly improve the ImgOpener performance, we could consider > adding another ImgOpener signature that lets you explicitly specify the file > format. > > > Bio-formats analyzes the folder. Some formats are multi-file. > > Indeed. And some files are even considered a different file format depending > on which other files are present in the same or nearby directories. > > Regards, > Curtis > > P.S. to Melissa: Johannes has some ideas for improving the TIFF reader > performance too, which he plans to explore over the next few days. We will > keep you posted on any progress. > > > On Wed, Feb 6, 2013 at 11:13 AM, Albert Cardona <[email protected]> wrote: > 2013/2/6 Tobias Pietzsch <[email protected]> > 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? > > > Yes, Bio-formats analyzes the folder. Some formats are multi-file. > > Albert > > -- > http://albert.rierol.net > http://www.ini.uzh.ch/~acardona/ > > -- > -- > 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
