Re: Montage java.lang.NegativeArraySizeException

Posted by Mark J. Chopping on Sep 01, 2015; 3:01am
URL: http://imagej.273.s1.nabble.com/Montage-java-lang-NegativeArraySizeException-tp5014201p5014212.html

The problem seems to have been a conflict between Montage and xvfb, so I have a partial solution: run the batch job in X11 without xvfb, like this:

~/ImageJ/jre/bin/java -Xmx4096m -jar ~/ImageJ/ij.jar -ijpath ~/ImageJ -batch mosaci_macro.ijm path/base > MLOG2 &

Result:

$ more MLOG2
...
Window Size:  800 x 800
SrcCols  =43176
SrcRows  =32636
xLocs     :  53
yLocs     :  40
numfiles  :  2120
Mosaicing the 2120 (53 x 40) images...
Image Sequence run; doing Make Montage...
Mosaic completed.

$ ls -l
 1356800240 Aug 31 22:54 Mosaiced_image.tif

This is great: although it means that I have to keep an X session alive rather than completely backgrounding all the jobs, at least I can run many jobs without intervention, if only sequentially (on each VM).

Many thanks to Curtis Rueden and John Hayes for excellent suggestions.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html