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<div>Hi,</div>
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<div>Thank you for your suggestion.</div>
<div>We have updated one of our PR’s to include your suggestion,</div>
<div><a href="https://github.com/openmicroscopy/bioformats/pull/1783">https://github.com/openmicroscopy/bioformats/pull/1783</a> </div>
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<div>Should mostly make it to our next stable release (Bio-Formats 5.1.2).</div>
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<div>Best,</div>
<div>Balaji</div>
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<div style="color: rgb(40, 40, 40);"><span style="background-color: rgb(255, 255, 255);">__________________</span></div>
<div style="color: rgb(40, 40, 40);">
<p style="margin-top: 0px; margin-bottom: 0px;">Mr Balaji Ramalingam</p>
<p style="margin-top: 0px; margin-bottom: 0px;">Software Developer<br>
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<p style="margin-top: 0px; margin-bottom: 0px;">OME Team</p>
<p style="margin-top: 0px; margin-bottom: 0px;">College of Life Sciences</p>
<p style="margin-top: 0px; margin-bottom: 0px;">University of Dundee</p>
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<span style="font-weight:bold">From: </span>Simon Blanchoud <<a href="mailto:simon.blanchoud@otago.ac.nz">simon.blanchoud@otago.ac.nz</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 7 May 2015 04:15<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-devel] Input java flags for command line tools<br>
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<div bgcolor="#FFFFFF" text="#000000">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 QA 11011):<br>
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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>
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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>
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./bfconvert -stitch ./tmp_folder/tmp_img1.jpg M-flow1.ome.tiff<br>
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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>
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(And yes, I then get a standard heap space error, for which I needed to increase the allocated space using -Xmx)<br>
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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>
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# Prepare the flags.<br>
if [ -z "$BF_FLAGS" ]<br>
then<br>
BF_FLAGS=""<br>
fi<br>
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In case you find this relevant !<br>
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Cheers,<br>
Simon<br>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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