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mmzeineh

bUnwarpJ question

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

Re: bUnwarpJ question

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

mmzeineh

Re: bUnwarpJ question

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

Re: bUnwarpJ question

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
>

mmzeineh

Re: bUnwarpJ question

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

Re: bUnwarpJ question

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
>

mmzeineh

Re: bUnwarpJ question

That finally worked!

Must have needed to find something else in the plugins directory!

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 27, 2013, at 7:52 AM, Ignacio Arganda-Carreras wrote:

> 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

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