Re: Parallel Iterative Deconvolution

Posted by ctrueden on Dec 24, 2016; 11:25am
URL: http://imagej.273.s1.nabble.com/Parallel-Iterative-Deconvolution-tp5013104p5017812.html

Hi Lara,

If you are using Fiji, you can use the "Find Jar For Class" command (press
L for the Command Finder, then type "Find Jar").

For the class name, put "edu.emory.mathcs.utils.ConcurrencyUtils" and hit
enter. It will list the JARs which contain it.

In my Fiji installation, without Parallel Iterative Deconvolution
installed, I receive:

The class edu.emory.mathcs.utils.ConcurrencyUtils is contained in
/Applications/Fiji.app/jars/jtransforms-2.4.jar

In my Fiji installation, I was able to make the PID plugin run by moving
away jtransforms-2.4.jar out of the jars folder.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
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On Fri, Dec 23, 2016 at 2:18 PM, lzsw <[hidden email]> wrote:

> I am running ImageJ 1.51h, Java 1.8.0_66 64bit and installed Parallel
> Iterative Deconvolution (parallelcolt-0.9.4.jar,
> parallel_iterative_deconvolution-1.12.jar, along with all the other .jars)
> and have the exact same error:
>
> java.lang.NoSuchMethodError:
> edu.emory.mathcs.utils.ConcurrencyUtils.submit(Ljava/
> util/concurrent/Callable;)Ljava/util/concurrent/Future;
>         at cern.colt.matrix.tfloat.impl.DenseFloatMatrix2D.
> getMaxLocation(Unknown
> Source)
>         at edu.emory.mathcs.restoretools.iterative.psf.FloatPSF2D.<
> init>(Unknown
> Source)
>         at
> edu.emory.mathcs.restoretools.iterative.psf.FloatPSFMatrix2D.<init>(
> Unknown
> Source)
>         at
> edu.emory.mathcs.restoretools.iterative.AbstractFloatIterativeDeconvol
> ver2D.<init>(Unknown
> Source)
>         at
> edu.emory.mathcs.restoretools.iterative.mrnsd.
> MRNSDFloatIterativeDeconvolver2D.<init>(Unknown
> Source)
>         at
> edu.emory.mathcs.restoretools.iterative.ParallelIterativeDeconvolution
> 2D$MainPanel$DeconvolveButtonActionListener$1.run(Unknown
> Source)
>         at java.lang.Thread.run(Thread.java:745)
>
>
>
> I've searched my plugins folder for parallelcolt and found only one
> version.
> I'm not sure what else might be going on.
> Thanks,
> Lara
>
>
> Piotr Wendykier-2 wrote
> > Hi Tim,
> >
> > You have multiple versions of Parallel Colt in the plugins directory.
> > You need to remove other versions and keep only the one in
> > ParallelIterativeDeconvolution directory.
> >
> > Piotr
> >
> > On Wed, Jun 10, 2015 at 9:46 PM, Feinstein, Timothy N &lt;
>
> > tnf8@
>
> > &gt; wrote:
> >> Hi all,
> >>
> >> I love Piotr Wendykier's deconvolution plugin for Fiji, but it stopped
> >> working today (see error message below).  Is it possible that something
> >> updated in Fiji (e.g., parallelcolt) and made it no longer compatible?
> I
> >> am trying to create a simple workflow for non-imaging specialists.
> >>
> >> java.lang.NoSuchMethodError:
> >> edu.emory.mathcs.utils.ConcurrencyUtils.submit(Ljava/
> util/concurrent/Callable;)Ljava/util/concurrent/Future;
> >> at cern.colt.matrix.tfloat.impl.DenseFloatMatrix3D.
> getMaxLocation(Unknown
> >> Source)
> >> at edu.emory.mathcs.restoretools.iterative.psf.FloatPSF3D.
> > <init>
> > (Unknown Source)
> >> at edu.emory.mathcs.restoretools.iterative.psf.FloatPSFMatrix3D.
> > <init>
> > (Unknown Source)
> >> at
> >> edu.emory.mathcs.restoretools.iterative.AbstractFloatIterativeDeconvol
> ver3D.
> > <init>
> > (Unknown Source)
> >> at
> >> edu.emory.mathcs.restoretools.iterative.mrnsd.
> MRNSDFloatIterativeDeconvolver3D.
> > <init>
> > (Unknown Source)
> >> at
> >> edu.emory.mathcs.restoretools.iterative.ParallelIterativeDeconvolution
> 3D$MainPanel$DeconvolveButtonActionListener$1.run(Unknown
> >> Source)
> >> at java.lang.Thread.run(Thread.java:695)
> >>
> >> Thanks,
> >>
> >>
> >> Tim
> >>
> >> Timothy Feinstein, Ph.D.
> >> Research Scientist
> >> University of Pittsburgh Department of Developmental Biology
> >>
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
>
>
> --
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> com/Parallel-Iterative-Deconvolution-tp5013104p5017811.html
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>
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