Re: JAVA error messages

Posted by Mark Adelman (Work) on Apr 04, 2011; 5:11pm
URL: http://imagej.273.s1.nabble.com/JAVA-error-messages-tp3684729p3684735.html

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.assignPixelsToMatrix(Unknown
>>>> Source)
>>>>        at
>>>> edu
>>>> .emory
>>>> .mathcs
>>>> .restoretools
>>>> .spectral.AbstractFloatSpectralDeconvolver3D.<init>(Unknown
>>>> Source)
>>>>        at
>>>> edu
>>>> .emory
>>>> .mathcs
>>>> .restoretools.spectral.tik.FloatReflexiveTikhonov3D.<init>(Unknown
>>>> Source)
>>>>        at
>>>> edu
>>>> .emory
>>>> .mathcs.restoretools.spectral.ParallelSpectralDeconvolution3D
>>>> $MainPanel$DeconvolveButtonActionListener$1.run(Unknown
>>>> Source)
>>>>        at java.lang.Thread.run(Thread.java:655)
>>>>
>>>
>