Re: parallel iterative deconvolution

Posted by SteveWest on Oct 20, 2016; 9:25am
URL: http://imagej.273.s1.nabble.com/parallel-iterative-deconvolution-tp5004620p5017429.html

Hi all, I thought I would post this in reply to a similar error.

I am running ParallelITerativeDeconvolution (v1.12) in FIJI on various machines, and they are all giving similar error messages.

On a windows and Debian machine, the errors halt the processing - I have yet to look into them in detail, but I suspect they are the same problem as listed here, and I will try to remove any extra copies of parallel colt.

However, on my mac (FIJI running ij-1.50b, java 1.8.0_60 64bit) I get the following Exception:

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 50000000
        at java.util.concurrent.FutureTask.report(FutureTask.java:122)
        at java.util.concurrent.FutureTask.get(FutureTask.java:192)
        at edu.emory.mathcs.utils.ConcurrencyUtils.waitForCompletion(Unknown Source)
        at edu.emory.mathcs.restoretools.iterative.wpl.WPLFloatIterativeDeconvolver3D.convolveFD(Unknown Source)
        at edu.emory.mathcs.restoretools.iterative.wpl.WPLFloatIterativeDeconvolver3D.deconvolve(Unknown Source)
        at edu.emory.mathcs.restoretools.iterative.ParallelIterativeDeconvolution3D$MainPanel$DeconvolveButtonActionListener$1.run(Unknown Source)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 50000000
        at edu.emory.mathcs.restoretools.iterative.wpl.WPLFloatIterativeDeconvolver3D$1.run(Unknown Source)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

It it thrown with the initiation of WPL and with each iteration. It occurs with any size of image.

Interestingly, the algorithm still manages to run.  It disappears when I run it on a "bare-bones" version of ImageJ - so there must be a clash with some class in FIJI.  It is still present if I use java 1.6 with FIJI.  I cannot find any extra jars of either "colt" or "parallel colt" in my build of FIJI..  It looks like an error associated with the ConcurrencyUtils class in ParallelIterativeDeconvolution - any ideas what is causing the problem?

Cheers, SJ.