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Hi all,<br>
<br>
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
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QA 11011):<br>
<br>
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<br>
<br>
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:<br>
<br>
./bfconvert -stitch ./tmp_folder/tmp_img1.jpg M-flow1.ome.tiff<br>
<br>
I get a java out of memory error:<br>
java.lang.OutOfMemoryError: GC overhead limit exceeded<br>
<br>
Turns out that (thanks Google), this issue can be solved by using
the following JVM flag:<br>
-XX:+UseConcMarkSweepGC <br>
<br>
(And yes, I then get a standard heap space error, for which I needed
to increase the allocated space using -Xmx)<br>
<br>
Anyway, finally to the point of this email:<br>
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):<br>
<br>
# Prepare the flags.<br>
if [ -z "$BF_FLAGS" ]<br>
then<br>
BF_FLAGS=""<br>
fi<br>
<br>
In case you find this relevant !<br>
<br>
Cheers,<br>
Simon<br>
<br>
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