Problem to save as DICOM with Tudor dicom tools

[Daniel Hornung]

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.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

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>(PlugInFilterRunner.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.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

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>(PlugInFilterRunner.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>(PlugInFilterRunner.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


--
Max-Planck-Institute for Dynamics and Self-Organization
Research Group Biomedical Physics

Am Fassberg 17
D-37077 Goettingen
([phone]

You can obtain my public key 0xF197B128 from all keyservers, e.g. pgp.mit.edu
Fingerprint: 9698 BDD4 71CC 1274 B7E2  2049 1EDD 012D F197 B128

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

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
>
>
> --
> Max-Planck-Institute for Dynamics and Self-Organization
> Research Group Biomedical Physics
>
> Am Fassberg 17
> D-37077 Goettingen
> ([phone]
>
> You can obtain my public key 0xF197B128 from all keyservers, e.g.
> pgp.mit.edu
> Fingerprint: 9698 BDD4 71CC 1274 B7E2  2049 1EDD 012D F197 B128
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Herbie]

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
>>
>>
>> --
>> Max-Planck-Institute for Dynamics and Self-Organization
>> Research Group Biomedical Physics
>>
>> Am Fassberg 17
>> D-37077 Goettingen
>> ([phone]
>>
>> You can obtain my public key 0xF197B128 from all keyservers, e.g.
>> pgp.mit.edu
>> Fingerprint: 9698 BDD4 71CC 1274 B7E2  2049 1EDD 012D F197 B128
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jan Eglinger]

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
>>>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Herbie]

Well Jan,

as far as I understand, I'd only need to put the correct version of a
library to the plugins folder of ImageJ -- no?

I use do so with many plugins that I use and update on a regular basis,
e.g. TransformJ that needs Imagescience. So what makes this case so special?

I feel that things become more complicated these days, but I simply may
not be in the know of the current and sophisticated mechanisms.

Best

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 16.08.16 um 10:45 schrieb Jan Eglinger:

> 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
>>>>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Salim Kanoun]

Hi all,

I just take the opportunity to say that we have recently made a DICOM
writer service in our PET/CT viewer project (project lead by Ilan Tal) see
http://petctviewer.org/index.php/feature/dicom-writing

We have designed it to re-write in DICOM modified PET and CT series. We
havn't tested other input data yet but let us know if you find issues in
Dicom writing.

Best regards,

Salim

2016-08-16 10:45 GMT+02:00 Jan Eglinger <[hidden email]>:

> 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.PlugInFilterR
>>>> unner.<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.PlugInFilterR
>>>> unner.<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.PlugInFilterR
>>>> unner.<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
>>>>
>>>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Daniel Hornung]

On Montag, 15. August 2016 13:59:59 CEST Curtis Rueden wrote:
> 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.

Yes, that's what I tried as well (renaming) and it worked fine for me so far
(until the next update check, which then of course tries to download the
"missing" file again).

Cheers,
Daniel

--
Max-Planck-Institute for Dynamics and Self-Organization
Research Group Biomedical Physics

Am Fassberg 17
D-37077 Goettingen
([phone]

You can obtain my public key 0xF197B128 from all keyservers, e.g. pgp.mit.edu
Fingerprint: 9698 BDD4 71CC 1274 B7E2  2049 1EDD 012D F197 B128

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenneth Sloan-2]

Count me as one anxiously waiting for the day when DICOM output is “easy”.  It’s something I would find convenient - but not worth constant monitoring and maintaining the proper mix of plugins.
--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On Aug 16, 2016, at 07:27 , Daniel Hornung <[hidden email]> wrote:
>
> On Montag, 15. August 2016 13:59:59 CEST Curtis Rueden wrote:
>> 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.
>
> Yes, that's what I tried as well (renaming) and it worked fine for me so far
> (until the next update check, which then of course tries to download the
> "missing" file again).
>
> Cheers,
> Daniel
>
> --
> Max-Planck-Institute for Dynamics and Self-Organization
> Research Group Biomedical Physics
>
> Am Fassberg 17
> D-37077 Goettingen
> ([phone]
>
> You can obtain my public key 0xF197B128 from all keyservers, e.g. pgp.mit.edu
> Fingerprint: 9698 BDD4 71CC 1274 B7E2  2049 1EDD 012D F197 B128
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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