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Parallel Iterative Deconvolution

TimFeinstein
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.AbstractFloatIterativeDeconvolver3D.<init>(Unknown Source)
at edu.emory.mathcs.restoretools.iterative.mrnsd.MRNSDFloatIterativeDeconvolver3D.<init>(Unknown Source)
at edu.emory.mathcs.restoretools.iterative.ParallelIterativeDeconvolution3D$MainPanel$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


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Re: Parallel Iterative Deconvolution

Piotr Wendykier-2
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 <[hidden email]> 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.AbstractFloatIterativeDeconvolver3D.<init>(Unknown Source)
> at edu.emory.mathcs.restoretools.iterative.mrnsd.MRNSDFloatIterativeDeconvolver3D.<init>(Unknown Source)
> at edu.emory.mathcs.restoretools.iterative.ParallelIterativeDeconvolution3D$MainPanel$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

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Re: Parallel Iterative Deconvolution

lzsw
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.AbstractFloatIterativeDeconvolver2D.<init>(Unknown Source)
        at edu.emory.mathcs.restoretools.iterative.mrnsd.MRNSDFloatIterativeDeconvolver2D.<init>(Unknown Source)
        at edu.emory.mathcs.restoretools.iterative.ParallelIterativeDeconvolution2D$MainPanel$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 <[hidden email]> 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.AbstractFloatIterativeDeconvolver3D.<init>(Unknown Source)
> at edu.emory.mathcs.restoretools.iterative.mrnsd.MRNSDFloatIterativeDeconvolver3D.<init>(Unknown Source)
> at edu.emory.mathcs.restoretools.iterative.ParallelIterativeDeconvolution3D$MainPanel$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

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Re: Parallel Iterative Deconvolution

ctrueden
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

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LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


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
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/Parallel-Iterative-Deconvolution-tp5013104p5017811.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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