NDPI support / bioformat

Mathieu Malaterre mathieu.malaterre at gmail.com
Fri Jul 27 11:50:02 EDT 2012


On Tue, Jul 17, 2012 at 3:07 PM, Yves Sucaet <sucaet at histogenex.com> wrote:
> Are you using a 32-bit or 64-bit jvm? Can you increase the heapspace even
> larger? Try 2048 or even 4096 instead of 1024 and see if that works.

Just for reference. I have been trying:

$ cat bfview
  java -XX:+HeapDumpOnOutOfMemoryError -Xms64m -Xmx4096m -cp
"$DIR":"$DIR/bio-formats.jar":"$DIR/loci_tools.jar" $PROG "$@"

Still with no luck. I have 16Gb of RAM and I was trying to open a
140Mb ndpi image.

It still fails with:

Populating OME metadata
java.lang.OutOfMemoryError: Java heap space
Dumping heap to java_pid18851.hprof ...
Heap dump file created [1701425587 bytes in 8.355 secs]
Exception in thread "ImageViewer-Opener" java.lang.OutOfMemoryError:
Java heap space
	at loci.formats.gui.AWTImageTools.makeRGBImage(AWTImageTools.java:576)
	at loci.formats.gui.AWTImageTools.makeImage(AWTImageTools.java:207)
	at loci.formats.gui.AWTImageTools.makeImage(AWTImageTools.java:494)
	at loci.formats.gui.AWTImageTools.openImage(AWTImageTools.java:782)
	at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:94)
	at loci.formats.gui.BufferedImageReader.openImage(BufferedImageReader.java:77)
	at loci.formats.gui.ImageViewer.open(ImageViewer.java:347)
	at loci.formats.gui.ImageViewer$1.run(ImageViewer.java:802)


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