Assistant Professor, Dept. of Radiology
Lucas Center for Imaging, Rm. P271
> Weird! That should have worked as long as your paths are correct...
>
> Can you try running the command from the plugins directory and typing
>
> java -Xmx512m -cp .:../jars/ij-1.48a.jar:bUnwarpJ_-2.6.1-SNAPSHOT.jar
> bunwarpj.bUnwarpJ_ -help
>
> ?
>
>
>
> On Sat, Aug 24, 2013 at 12:00 AM, Michael Zeineh <
[hidden email]>wrote:
>
>> Hi Ignacio,
>>
>> Tried this command (after upgrading Fiji):
>> java -Xmx512m -cp
>> ~/bin/Fiji.app/jars/ij-1.48a.jar:~/bin/Fiji.app/plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar
>> bunwarpj.bUnwarpJ_ -help
>>
>> And got this result:
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> bunwarpj/bUnwarpJ_
>> Caused by: java.lang.ClassNotFoundException: bunwarpj.bUnwarpJ_
>> at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
>> Could not find the main class: bunwarpj.bUnwarpJ_. Program will exit.
>>
>>
>> Michael Zeineh, M.D.-Ph.D.
>> Assistant Professor, Dept. of Radiology
>> Stanford University
>> Lucas Center for Imaging, Rm. P271
>> 1201 Welch Road
>> Stanford CA 94305-5488
>> t: 650-721-1419
>> c: 650-722-2235
>> f: 650-723-5795
>>
[hidden email]
>>
>> Administrative Contact:
>> Scott McIntosh
>>
[hidden email]
>>
>>
>> On Aug 23, 2013, at 12:19 PM, Ignacio Arganda-Carreras wrote:
>>
>>> Those * should not be there (my fault for using the rich editor). Try
>> this:
>>>
>>> java -Xmx512m -cp
>>> ~/bin/Fiji.app/jars/ij-1.47q.jar:~/bin/Fiji.app/plugins/bUnwarpJ_.jar
>>> bunwarpj.bUnwarpJ_ -help
>>>
>>>
>>> On Wed, Aug 21, 2013 at 6:17 PM, Michael Zeineh <
[hidden email]
>>> wrote:
>>>
>>>> Hi Ignacio,
>>>>
>>>> I get the same error: "Could not find the main class:
>> *bunwarpj*.bUnwarpJ_"
>>>>
>>>> On Aug 21, 2013, at 12:25 AM, Ignacio Arganda-Carreras wrote:
>>>>
>>>>> Hello Michael,
>>>>>
>>>>> Can you try typing
>>>>>
>>>>> java -Xmx512m -cp
>>>> ~/bin/Fiji.app/jars/ij-1.47q.jar:~/bin/Fiji.app/plugins/
>>>>> bUnwarpJ_.jar *bunwarpj*.bUnwarpJ_ -help
>>>>>
>>>>> instead?
>>>>>
>>>>> ignacio
>>>>>
>>>>>
>>>>> On Tue, Aug 20, 2013 at 6:28 PM, Michael Zeineh <
[hidden email]
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I am trying to multithread bUnwarpJ on a cluster. I am trying two
>>>>>> approaches, and running into difficulties with both:
>>>>>>
>>>>>> 1. I would like to be able to run bunwarpj from within a python
>> script.
>>>> I
>>>>>> can do this right now, except I cannot figure out the command for
>>>> importing
>>>>>> bUnwarpJ at the beginning of the script. If I simply type "import
>>>> bunwarpj"
>>>>>> then it can't find the module. I can't figure out where to pull it
>> from,
>>>>>> i.e. "from ij.plugin import bunwarpj" doesn't work. The only thing
>> that
>>>>>> works is actually going to the menu and running
>>>>>> Plugins->Registration->bUnwarpJ, then running my python script. Would
>> be
>>>>>> great to be able to start it directly from my python script by
>>>> importing it
>>>>>> directly.
>>>>>>
>>>>>> 2. I cannot get bunwarpj to work from the UNIX command line per the
>>>>>> description in the web page:
>>>>>>
>>>>>> Here is what I try on a redhat linux box:
>>>>>> java -Xmx512m -cp
>>>>>> ~/bin/Fiji.app/jars/ij-1.47q.jar:~/bin/Fiji.app/plugins/bUnwarpJ_.jar
>>>>>> bUnwarpJ_ -help
>>>>>>
>>>>>> I get a "Could not find the main class: bUnwarpJ_. Program will exit."
>>>>>>
>>>>>> I played around with a lot of paths, couldn't get anything to work.
>>>>>> bUnwarpJ works totally fine from the GUI within Fiji on this computer
>>>>>>
>>>>>> Thank you for any help. I wonder if these are both the same problem.
>>>>>>
>>>>>> Michael Zeineh
>>>>>> --
>>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Ignacio Arganda-Carreras, Ph.D.
>>>>> Seung's lab, 46-5065
>>>>> Department of Brain and Cognitive Sciences
>>>>> Massachusetts Institute of Technology
>>>>> 43 Vassar St.
>>>>> Cambridge, MA 02139
>>>>> USA
>>>>>
>>>>> Phone: (001) 617-324-3747
>>>>> Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html>>>>>
>>>>> --
>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>
>>>> Michael Zeineh, M.D.-Ph.D.
>>>> Assistant Professor, Dept. of Radiology
>>>> Stanford University
>>>> Lucas Center for Imaging, Rm. P271
>>>> 1201 Welch Road
>>>> Stanford CA 94305-5488
>>>> t: 650-721-1419
>>>> c: 650-722-2235
>>>> f: 650-723-5795
>>>>
[hidden email]
>>>>
>>>> Administrative Contact:
>>>> Scott McIntosh
>>>>
[hidden email]
>>>>
>>>>
>>>>
>>>> --
>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>
>>>
>>>
>>>
>>> --
>>> Ignacio Arganda-Carreras, Ph.D.
>>> Seung's lab, 46-5065
>>> Department of Brain and Cognitive Sciences
>>> Massachusetts Institute of Technology
>>> 43 Vassar St.
>>> Cambridge, MA 02139
>>> USA
>>>
>>> Phone: (001) 617-324-3747
>>> Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Seung's lab, 46-5065
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St.
> Cambridge, MA 02139
> USA
>
> Phone: (001) 617-324-3747
> Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html