ImageJ - Re: Problem to save as DICOM with Tudor dicom tools

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Re: Problem to save as DICOM with Tudor dicom tools

Posted by Jan Eglinger on
URL: http://imagej.273.s1.nabble.com/Problem-to-save-as-DICOM-with-Tudor-dicom-tools-tp5017013p5017019.html

Dear Herbie,

as Curtis nicely explained, the problem is caused by the presence of two
different versions of the same library. In this case the DICOM tools and
the Bio-Formats plugins both depend on `jgoodies-forms` but on different
versions of those.

As "core ImageJ" does not ship this library, users who are using ImageJ
without any additional plugins will not have the problem.
However, it will likely occur for anyone who uses Bio-Formats and wants
to install the DICOM tools.

I agree with Curtis that if DICOM Tools were provided by an update site,
we could make installation much easier for users by ensuring that
version skews like this one do not happen.

Cheers,
Jan

On 16.08.2016 10:27, Herbie wrote:

> Just curious,
>
> is this a Fiji-problem or does it hold for plain ImageJ as well?
>
> Good day
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::
> Am 15.08.16 um 20:59 schrieb Curtis Rueden:
>> Hi Daniel,
>>
>>> There was a problem with the class
>>> com.jgoodies.forms.builder.ButtonBarBuilder which can be found here:
>>> /home/daniel/programs/Fiji.app/jars/jgoodies-forms-1.7.2.jar
>>> /home/daniel/programs/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar
>>
>> This means that the Tudor DICOM Tools are shipping with a different (and
>> incompatible) version of the library called JGoodies Forms.
>>
>> As a workaround, you can try removing jars/jgoodies-forms-1.7.2.jar
>> from in
>> your local installation; the one that Tudor DICOM Tools needs is in
>> plugins/TudorDICOMLibs/forms-1.0.6.jar.
>>
>>> Is it maybe possible somehow to tell the plugin to look into its "own"
>>> forms.jar instead of the preinstalled file (Fiji.app/jars/jgoodies-
>>> forms-1.7.2.jar)?
>>
>> Unfortunately not. At least, not without a major change to the ImageJ
>> infrastructure, which would make it more complex.
>>
>> The best way to fix this is for Tudor DICOM Tools to be structured as an
>> ImageJ update site compatible with ImageJ2 and Fiji. I have suggested
>> this
>> path to the authors in the past, but they ignore these mailing list
>> threads
>> [1, 2]. Ways forward include:
>>
>> - email the Tudor DICOM Tools authors directly to renew the request
>> - set up a third party update site for the Tudor DICOM Tools,
>> maintained by
>> someone in the community
>>
>> See also:
>> http://imagej.net/DICOM
>>
>> It would be great, if you get the Tudor DICOM Tools working, if you could
>> at least edit the above wiki page with hints on how to do so.
>>
>> Regards,
>> Curtis
>>
>> --
>> Curtis Rueden
>> 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/
>>
>> [1] http://imagej.1557.x6.nabble.com/oib-to-DICOM-tt5016100.html#a5016154
>> [2]
>> http://imagej.1557.x6.nabble.com/czi-DICOM-or-mrb-tp5015970p5016237.html
>>
>>
>> On Mon, Aug 15, 2016 at 4:47 AM, Daniel Hornung
>> <[hidden email]>
>> wrote:
>>
>>> Hi everyone,
>>>
>>> I am trying to save tiff stacks as DICOM, and downloaded and
>>> installed the
>>> latest Tudor DICOM Tools (version 1.9.30).
>>>
>>> When calling File > Save as > Save DICOM, I get the following error:
>>>
>>> ==========
>>>
>>> There was a problem with the class com.jgoodies.forms.builder.But
>>> tonBarBuilder
>>> which can be found here:
>>> /home/daniel/programs/Fiji.app/jars/jgoodies-forms-1.7.2.jar
>>> /home/daniel/programs/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar
>>>
>>> WARNING: multiple locations found!
>>> java.lang.NoSuchMethodError:
>>> com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
>>> at Save_As_Dicom.setup(Save_As_Dicom.java:100)
>>> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunne
>>> r.java:48)
>>> at ij.IJ.runUserPlugIn(IJ.java:219)
>>> at ij.IJ.runPlugIn(IJ.java:181)
>>> at ij.Executer.runCommand(Executer.java:137)
>>> at ij.Executer.run(Executer.java:66)
>>> at java.lang.Thread.run(Thread.java:662)
>>>
>>> java.lang.NoSuchMethodException: Could not find method
>>> com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
>>> There was a problem with the class com.jgoodies.forms.builder.But
>>> tonBarBuilder
>>> which can be found here:
>>> /home/daniel/programs/Fiji.app/jars/jgoodies-forms-1.7.2.jar
>>> /home/daniel/programs/Fiji.app/plugins/TudorDICOMLibs/forms-1.0.6.jar
>>>
>>> WARNING: multiple locations found!
>>> java.lang.NoSuchMethodError:
>>> com.jgoodies.forms.builder.ButtonBarBuilder.addGlue()V
>>> at Save_As_Dicom.setup(Save_As_Dicom.java:100)
>>> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunne
>>> r.java:48)
>>> at ij.IJ.runUserPlugIn(IJ.java:219)
>>> at ij.IJ.runPlugIn(IJ.java:181)
>>> at ij.Executer.runCommand(Executer.java:137)
>>> at ij.Executer.run(Executer.java:66)
>>> at java.lang.Thread.run(Thread.java:662)
>>>
>>> at Save_As_Dicom.setup(Save_As_Dicom.java:100)
>>> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunne
>>> r.java:48)
>>> at ij.IJ.runUserPlugIn(IJ.java:219)
>>> at ij.IJ.runPlugIn(IJ.java:181)
>>> at ij.Executer.runCommand(Executer.java:137)
>>> at ij.Executer.run(Executer.java:66)
>>> at java.lang.Thread.run(Thread.java:662)
>>>
>>>
>>> ==========
>>>
>>> My Fiji distribution is up-to-date. Can anyone reproduce this
>>> problem, or
>>> knows a workaround?
>>>
>>> Is it maybe possible somehow to tell the plugin to look into its "own"
>>> forms.jar instead of the preinstalled file (Fiji.app/jars/jgoodies-
>>> forms-1.7.2.jar)?
>>>
>>> Note that the plugin also came with its own version of the 3D viewer and
>>> loci_tools.jar, which I renamed to prevent naming conflicts at startup.
>>>
>>> Thanks!
>>> Daniel
>>>

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