[ome-devel] Input java flags for command line tools

[Simon Blanchoud]

Hi all,

I'm still playing with my .avi recordings that I want to convert to 
ome.tiff stacks. To do so, I first extract the key frames from the 
recording using FFMPEG (file QA 11011):

ffmpeg -i M-flow1.avi -y -vf select="eq(pict_type\,PICT_TYPE_I)" -vsync 
2 -qscale:v 2 -f image2 ./tmp_folder/tmp_img%d.jpg

Turns out that those avi recordings contain quite a lot of frames 
(several thousands actually), and so, when I afterwards tried to stitch 
them up using:

./bfconvert -stitch ./tmp_folder/tmp_img1.jpg M-flow1.ome.tiff

I get a java out of memory error:
java.lang.OutOfMemoryError: GC overhead limit exceeded

Turns out that (thanks Google), this issue can be solved by using the 
following JVM flag:
-XX:+UseConcMarkSweepGC

(And yes, I then get a standard heap space error, for which I needed to 
increase the allocated space using -Xmx)

Anyway, finally to the point of this email:
Turns out that there is currently no way to provide additional flags to 
the JVM for the bio-formats command line tools ! Turns out that's very 
easily fixed by adding the following few lines at the beginning of bf.sh 
(just as for BF_MEM_MAX):

# Prepare the flags.
if [ -z "$BF_FLAGS" ]
then
   BF_FLAGS=""
fi

In case you find this relevant !

Cheers,
Simon

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