http://imagej.273.s1.nabble.com/JAVA-error-messages-tp3684729p3684737.html
That did it! No error messages and all the algorithms ran. I'll now
be able to explore each in some detail with a variety of data sets.
> I would remove parallelcolt-0.9.jar from
> ParallelSpectralDeconvolution, remove ParallelIterativeDeconvolution
> directory and then install the latest version of
> ParallelIterativeDeconvolution that comes with parallelcolt-0.9.jar.
>
> Piotr
>
> On Mon, Apr 4, 2011 at 12:11 PM, Mark Adelman (Work)
> <
[hidden email]> wrote:
>> Piotr -
>> There is no such file in the the main MM directory, nor in the
>> mmplugins
>> folder, nor in the plugins folder (this is the one with ImageJ
>> plugins).
>> But the folder for ParallelSpectralDecovolution (within plugins) has
>> "parallelcolt-0.9.jar" and the folder for
>> ParallelIterativeDecovolution
>> (within plugins) has "parallelcolt-0.7.2.jar". Should I remove
>> one (or
>> both) of these? Move one (or both)? If so, which should I move/
>> remove?
>> Thanks!
>> Mark
>>
>> From: Piotr Wendykier <
[hidden email]>
>> Date: April 4, 2011 11:05:39 AM EDT
>> To: ImageJ Interest Group <
[hidden email]>
>> Cc: "Mark Adelman (Work)" <
[hidden email]>
>> Subject: Re: JAVA error messages
>> Mark,
>> I'm the author of Parallel Spectral/Iterative Deconvolution plugins.
>> There is something wrong with the configuration of your Micro-
>> Manager 1.3.
>> You can try to search for parallelcolt*.jar in the plugins directory.
>> There should be only one file that matches this pattern.
>> I hope this helps,
>> Piotr
>>
>> On Mon, Apr 4, 2011 at 9:47 AM, Mark Adelman (Work)
>> <
[hidden email]> wrote:
>>
>> Can someone give me some guidance regarding JAVA error messages I am
>> getting? An example is included at the end of this message. Am
>> learning to
>> do some wide-field image deconvolution work. My platform is a
>> MacBook (2.13
>> GHz Intel Core 2 Duo, 4 GB MHz DDR2 SDRAM, OS 10.5.8). It is up-
>> to-date on
>> all Mac software updates (including the JAVA that Mac provides).
>> I am
>> running ImageJ 1.45d (under Micro-Manager 1.3). My knowledge of
>> JAVA,
>> programming, etc. is quite limited. Have been using an old confocal
>> microscopy (MRC600) data set as a test sample. Have gotten some
>> pretty nice
>> results using the plugins by Bob Dougherty (in the Deconvolution
>> folder) to
>> generate a PSF and to do Iterative 3D deconvolutions, first of the
>> confocal
>> set and then of some actual wide field data sets. I was also able
>> to run a
>> number of the plugins in the DeconvolutionLab folder. When I
>> tried Parallel
>> Iterative Deconvolutions a number of one line JAVA error messages
>> (about
>> thrown threads, exceptions, etc....) showed up. I moved on to
>> Parallel
>> Spectral Deconvolutions and, no matter what I tried, got long
>> error messages
>> (see example below) and the program locked. Can someone suggest
>> how to
>> figure out what I'm doing wrong? Have looked at the Wiki page and
>> done a
>> number of Google searches, to no avail. Am just starting to read
>> on JAVA
>> and other programming issues, but am a LONG way from being able to
>> resolve
>> this without some guidance from people more knowledgeable than
>> me. Thanks
>> in advance for any help!
>> Mark Adelman
>>
>> java.lang.NoSuchMethodError:
>> cern.colt.matrix.tfloat.FloatMatrix3D.size()J
>> at
>> edu.emory.mathcs.restoretools.spectral.FloatCommon3D.assignPixelsToMa
>> trix(Unknown
>> Source)
>> at
>> edu.emory.mathcs.restoretools.spectral.AbstractFloatSpectralDeconvolv
>> er3D.<init>(Unknown
>> Source)
>> at
>> edu.emory.mathcs.restoretools.spectral.tik.FloatReflexiveTikhonov3D.<
>> init>(Unknown
>> Source)
>> at
>> edu.emory.mathcs.restoretools.spectral.ParallelSpectralDeconvolution3
>> D$MainPanel$DeconvolveButtonActionListener$1.run(Unknown
>> Source)
>> at java.lang.Thread.run(Thread.java:655)
>>
>>
>>
>>