I executed the "Plugins - Examples - Downsample" 3 times, on images of 4000x3000 RGB.
Every time I closed the resulting smaller images (2000x1500) after saving them as PNG. The original images were open, each taking about 46 Mb of RAM. Fiji had 2.5 Gb of Xmx.
Upon executing the script for the fourth time I got the exception below, caused by out of heap space.



java.lang.reflect.InvocationTargetException
	at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.Command.runPlugIn(Command.java:146)
	at ij.Command.runCommand(Command.java:95)
	at ij.Executer.run(Executer.java:64)
	at ij.IJ.run(IJ.java:249)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.mozilla.javascript.MemberBox.invoke(Unknown Source)
	at org.mozilla.javascript.NativeJavaMethod.call(Unknown Source)
	at org.mozilla.javascript.optimizer.OptRuntime.call2(Unknown Source)
	at org.mozilla.javascript.gen.c12._c0(/home/albert/Programming/fiji/plugins//Examples/downsample_.js:99)
	at org.mozilla.javascript.gen.c12.call(/home/albert/Programming/fiji/plugins//Examples/downsample_.js)
	at org.mozilla.javascript.ContextFactory.doTopCall(Unknown Source)
	at org.mozilla.javascript.ScriptRuntime.doTopCall(Unknown Source)
	at org.mozilla.javascript.gen.c12.call(/home/albert/Programming/fiji/plugins//Examples/downsample_.js)
	at org.mozilla.javascript.gen.c12.exec(/home/albert/Programming/fiji/plugins//Examples/downsample_.js)
	at org.mozilla.javascript.Context.evaluateReader(Unknown Source)
	at Javascript.Refresh_Javascript_Scripts.runScript(Refresh_Javascript_Scripts.java:53)
	at Javascript.Refresh_Javascript_Scripts.runScript(Refresh_Javascript_Scripts.java:33)
	at common.RefreshScripts.run(RefreshScripts.java:284)
	at Javascript.Refresh_Javascript_Scripts.run(Refresh_Javascript_Scripts.java:22)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.Command.runPlugIn(Command.java:146)
	at ij.Command.runCommand(Command.java:95)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.OutOfMemoryError: Java heap space
	at ij.process.ColorProcessor.toFloat(ColorProcessor.java:1286)
	at ij.plugin.filter.GaussianBlur.blurGaussian(GaussianBlur.java:157)
	at ij.plugin.filter.GaussianBlur.run(GaussianBlur.java:130)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:256)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:105)
	at ij.IJ.runPlugIn(IJ.java:158)
	at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.Command.runPlugIn(Command.java:146)
	at ij.Command.runCommand(Command.java:95)
	at ij.Executer.run(Executer.java:64)
	at ij.IJ.run(IJ.java:249)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.mozilla.javascript.MemberBox.invoke(Unknown Source)
	at org.mozilla.javascript.NativeJavaMethod.call(Unknown Source)
	at org.mozilla.javascript.optimizer.OptRuntime.call2(Unknown Source)
	at org.mozilla.javascript.gen.c12._c0(/home/albert/Programming/fiji/plugins//Examples/downsample_.js:99)
	at org.mozilla.javascript.gen.c12.call(/home/albert/Programming/fiji/plugins//Examples/downsample_.js)
	at org.mozilla.javascript.ContextFactory.doTopCall(Unknown Source)
	at org.mozilla.javascript.ScriptRuntime.doTopCall(Unknown Source)
	at org.mozilla.javascript.gen.c12.call(/home/albert/Programming/fiji/plugins//Examples/downsample_.js)
	at org.mozilla.javascript.gen.c12.exec(/home/albert/Programming/fiji/plugins//Examples/downsample_.js)
	at org.mozilla.javascript.Context.evaluateReader(Unknown Source)
	at Javascript.Refresh_Javascript_Scripts.runScript(Refresh_Javascript_Scripts.java:53)
	at Javascript.Refresh_Javascript_Scripts.runScript(Refresh_Javascript_Scripts.java:33)
	at common.RefreshScripts.run(RefreshScripts.java:284)
	at Javascript.Refresh_Javascript_Scripts.run(Refresh_Javascript_Scripts.java:22)
	at ij.IJ.runUserPlugIn(IJ.java:183)




Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => amd64
  os.name => Linux
  os.version => 2.6.38-13-generic
  java.version => 1.6.0_21
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_21-b06
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 17.0-b16
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: You wanted never to be reminded.

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/albert/Programming/fiji/java/linux-amd64/jdk1.6.0_21/jre
  fiji.dir => /home/albert/Programming/fiji

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