ImageJ

Incorporating a plugin into the ij.jar file

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

5 messages Options

Dan McDonald

Incorporating a plugin into the ij.jar file

Dear List,

I would like to incorporate the Skeletonize (2D/3D) plugin into the ij.jar
file. I have been unsuccessful in finding a way to do so.

I have the Skeletonize (2D/3D) executable jar file located in my plugin
folder. I successfully run the plugin on a daily basis when I use ImageJ.
I cannot figure out how to add a plugin that is in my plugin folder to the
ij.jar.

I have "uncompressed" the ij.jar and placed the Skeletonize3D.class file in
the jar's plugin folder. I then went into the IJ Properties.txt file and
modified it to add Skeletonize (2D/3D) as a user plugin. As shown below:

# Install user plugins located in ij.jar to Plugins>User Plugins submenu

user_plugins01="Skeletonize (2D/3D)",ij.plugin.Skeletonize3D_

(I am not sure what the arguments above are supposed to be. I could not
find documentation on adding user plugins via the IJProperties.txt route.
What I did looked the closest to want other lines had in them.)

I then rezipped everything.

When next I startup ImageJ the plugin shows up on the user plugin menu as
expected.

Unfortunately I get the following error messages when I select the
skeletonize function.

ImageJ 1.51p; Java 1.8.0_141 [64-bit]; Linux 3.13.0-37-generic; 16MB of
22020MB (<1%)

java.lang.NoClassDefFoundError: ij/plugin/Skeletonize3D_ (wrong name:
Skeletonize3D_/Skeletonize3D_)

at java.lang.ClassLoader.defineClass1(Native Method)

at java.lang.ClassLoader.defineClass(ClassLoader.java:763)

at
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)

at
java.net.URLClassLoader.defineClass(URLClassLoader.java:467)

at java.net.URLClassLoader.access$100(URLClassLoader.java:73)

at java.net.URLClassLoader$1.run(URLClassLoader.java:368)

at java.net.URLClassLoader$1.run(URLClassLoader.java:362)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:361)

at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

at
sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)

at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:264)

at ij.IJ.runPlugIn(IJ.java:184)

at ij.Executer.runCommand(Executer.java:137)

at ij.Executer.run(Executer.java:66)

at java.lang.Thread.run(Thread.java:748)

I am not sure if my syntax is incorrect in IJProperties.txt or if I need to
do more than just drop a class file in the ij.jar plugin folder or both.

I am not a java person. Any assistance or pointers to documentation would
be much appreciated.

Thank you,

Dan

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

ctrueden

Re: Incorporating a plugin into the ij.jar file

Hi Dan,

Before we dive into technical details: could you describe why you want to
do this? What is your use case? Are you trying to make an "uber-JAR" [1]?
If so, why?

Regards,
Curtis

[1] https://imagej.net/Uber-JAR

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Fri, Apr 20, 2018 at 2:16 PM, Dan McDonald <mcdonalddw@
phenotypescreening.com> wrote:

> Dear List,
>
>
>
> I would like to incorporate the Skeletonize (2D/3D) plugin into the ij.jar
> file. I have been unsuccessful in finding a way to do so.
>
>
>
> I have the Skeletonize (2D/3D) executable jar file located in my plugin
> folder. I successfully run the plugin on a daily basis when I use ImageJ.
> I cannot figure out how to add a plugin that is in my plugin folder to the
> ij.jar.
>
>
>
> I have "uncompressed" the ij.jar and placed the Skeletonize3D.class file in
> the jar's plugin folder. I then went into the IJ Properties.txt file and
> modified it to add Skeletonize (2D/3D) as a user plugin. As shown below:
>
>
>
> # Install user plugins located in ij.jar to Plugins>User Plugins submenu
>
>
>
> user_plugins01="Skeletonize (2D/3D)",ij.plugin.Skeletonize3D_
>
>
>
> (I am not sure what the arguments above are supposed to be. I could not
> find documentation on adding user plugins via the IJProperties.txt route.
> What I did looked the closest to want other lines had in them.)
>
>
>
> I then rezipped everything.
>
>
>
> When next I startup ImageJ the plugin shows up on the user plugin menu as
> expected.
>
>
>
> Unfortunately I get the following error messages when I select the
> skeletonize function.
>
>
>
> ImageJ 1.51p; Java 1.8.0_141 [64-bit]; Linux 3.13.0-37-generic; 16MB of
> 22020MB (<1%)
>
> java.lang.NoClassDefFoundError: ij/plugin/Skeletonize3D_ (wrong name:
> Skeletonize3D_/Skeletonize3D_)
>
> at java.lang.ClassLoader.defineClass1(Native Method)
>
> at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
>
> at
> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
>
> at
> java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
>
> at java.net.URLClassLoader.access
> $100(URLClassLoader.java:73)
>
> at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
>
> at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
>
> at java.security.AccessController.doPrivileged(Native
> Method)
>
> at java.net.URLClassLoader.findCl
> ass(URLClassLoader.java:361)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
>
> at
> sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>
> at java.lang.Class.forName0(Native Method)
>
> at java.lang.Class.forName(Class.java:264)
>
> at ij.IJ.runPlugIn(IJ.java:184)
>
> at ij.Executer.runCommand(Executer.java:137)
>
> at ij.Executer.run(Executer.java:66)
>
> at java.lang.Thread.run(Thread.java:748)
>
>
>
> I am not sure if my syntax is incorrect in IJProperties.txt or if I need to
> do more than just drop a class file in the ij.jar plugin folder or both.
>
>
>
> I am not a java person. Any assistance or pointers to documentation would
> be much appreciated.
>
>
>
> Thank you,
>
>
>
> Dan
>
>
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Dan McDonald

Re: Incorporating a plugin into the ij.jar file

Hi Curtis,

I have a java application which runs ImageJ in a headless mode. I wrote all of the ImageJ macro code but not the java application itself. ImageJ was bundled with an older version of skeletonize. This ran just fine in my application. I get improved performance with Ignacio's new version.

I have used NetBeans to make simple changes to the Java application. I thought adding the Skeletonize3D plugin to the ImageJ internal plugins would be simple. But I just don't know enough to make it work.

Dan

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Friday, April 20, 2018 4:19 PM
To: [hidden email]
Subject: Re: Incorporating a plugin into the ij.jar file

Hi Dan,

Before we dive into technical details: could you describe why you want to
do this? What is your use case? Are you trying to make an "uber-JAR" [1]?
If so, why?

Regards,
Curtis

[1] https://imagej.net/Uber-JAR

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Fri, Apr 20, 2018 at 2:16 PM, Dan McDonald <mcdonalddw@
phenotypescreening.com> wrote:

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

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

ctrueden

Re: Incorporating a plugin into the ij.jar file

In reply to this post by ctrueden

Hi Dan,

Thanks for the additional details.

If I understand correctly, you are talking about using this project:

Plugins>Skeleton, "Skeletonize (2D/3D)"
sc.fiji.skeletonize3D.Skeletonize3D_
https://github.com/fiji/Skeletonize3D

In lieu of ImageJ1's built-in:

Process>Binary>Skeletonize
ij.plugin.filter.Binary("skel")

If so, why not simply depend on the Skeletonize3D_.jar library in addition
to ij.jar? Why do you need to create a modified ij.jar?

Is your application code published anywhere?

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Fri, Apr 20, 2018 at 4:16 PM, Dan McDonald <
[hidden email]> wrote:

> Hi Curtis,
>
> I have a java application which runs ImageJ in a headless mode. I wrote
> all of the ImageJ macro code but not the java application itself. ImageJ
> was bundled with an older version of skeletonize. This ran just fine in my
> application. I get improved performance with Ignacio's new version.
>
> I have used NetBeans to make simple changes to the Java application. I
> thought adding the Skeletonize3D plugin to the ImageJ internal plugins
> would be simple. But I just don't know enough to make it work.
>
> Dan
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Friday, April 20, 2018 4:19 PM
> To: [hidden email]
> Subject: Re: Incorporating a plugin into the ij.jar file
>
> Hi Dan,
>
> Before we dive into technical details: could you describe why you want to
> do this? What is your use case? Are you trying to make an "uber-JAR" [1]?
> If so, why?
>
> Regards,
> Curtis
>
> [1] https://imagej.net/Uber-JAR
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Fri, Apr 20, 2018 at 2:16 PM, Dan McDonald <mcdonalddw@
> phenotypescreening.com> wrote:
>
> > Dear List,
> >
> >
> >
> > I would like to incorporate the Skeletonize (2D/3D) plugin into the
> ij.jar
> > file. I have been unsuccessful in finding a way to do so.
> >
> >
> >
> > I have the Skeletonize (2D/3D) executable jar file located in my plugin
> > folder. I successfully run the plugin on a daily basis when I use
> ImageJ.
> > I cannot figure out how to add a plugin that is in my plugin folder to
> the
> > ij.jar.
> >
> >
> >
> > I have "uncompressed" the ij.jar and placed the Skeletonize3D.class file
> in
> > the jar's plugin folder. I then went into the IJ Properties.txt file and
> > modified it to add Skeletonize (2D/3D) as a user plugin. As shown below:
> >
> >
> >
> > # Install user plugins located in ij.jar to Plugins>User Plugins submenu
> >
> >
> >
> > user_plugins01="Skeletonize (2D/3D)",ij.plugin.Skeletonize3D_
> >
> >
> >
> > (I am not sure what the arguments above are supposed to be. I could not
> > find documentation on adding user plugins via the IJProperties.txt route.
> > What I did looked the closest to want other lines had in them.)
> >
> >
> >
> > I then rezipped everything.
> >
> >
> >
> > When next I startup ImageJ the plugin shows up on the user plugin menu as
> > expected.
> >
> >
> >
> > Unfortunately I get the following error messages when I select the
> > skeletonize function.
> >
> >
> >
> > ImageJ 1.51p; Java 1.8.0_141 [64-bit]; Linux 3.13.0-37-generic; 16MB of
> > 22020MB (<1%)
> >
> > java.lang.NoClassDefFoundError: ij/plugin/Skeletonize3D_ (wrong name:
> > Skeletonize3D_/Skeletonize3D_)
> >
> > at java.lang.ClassLoader.defineClass1(Native Method)
> >
> > at java.lang.ClassLoader.defineClass(ClassLoader.java:
> 763)
> >
> > at
> > java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
> >
> > at
> > java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
> >
> > at java.net.URLClassLoader.access
> > $100(URLClassLoader.java:73)
> >
> > at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
> >
> > at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
> >
> > at java.security.AccessController.doPrivileged(Native
> > Method)
> >
> > at java.net.URLClassLoader.findCl
> > ass(URLClassLoader.java:361)
> >
> > at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> >
> > at
> > sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
> >
> > at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> >
> > at java.lang.Class.forName0(Native Method)
> >
> > at java.lang.Class.forName(Class.java:264)
> >
> > at ij.IJ.runPlugIn(IJ.java:184)
> >
> > at ij.Executer.runCommand(Executer.java:137)
> >
> > at ij.Executer.run(Executer.java:66)
> >
> > at java.lang.Thread.run(Thread.java:748)
> >
> >
> >
> > I am not sure if my syntax is incorrect in IJProperties.txt or if I need
> to
> > do more than just drop a class file in the ij.jar plugin folder or both.
> >
> >
> >
> > I am not a java person. Any assistance or pointers to documentation
> would
> > be much appreciated.
> >
> >
> >
> > Thank you,
> >
> >
> >
> > Dan
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > 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
>

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

Dan McDonald

Re: Incorporating a plugin into the ij.jar file

Hi Curtis,

Thank you for the reply. I believe I had a faulty mental model of how to approach my goal. You have helped me understand that I am dealing with a java issue and not an ImageJ issue.

Best regards,

Dan

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Friday, April 20, 2018 5:33 PM
To: [hidden email]
Subject: Re: Incorporating a plugin into the ij.jar file

Hi Dan,

Thanks for the additional details.

If I understand correctly, you are talking about using this project:

Plugins>Skeleton, "Skeletonize (2D/3D)"
sc.fiji.skeletonize3D.Skeletonize3D_
https://github.com/fiji/Skeletonize3D

In lieu of ImageJ1's built-in:

Process>Binary>Skeletonize
ij.plugin.filter.Binary("skel")

If so, why not simply depend on the Skeletonize3D_.jar library in addition
to ij.jar? Why do you need to create a modified ij.jar?

Is your application code published anywhere?

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Fri, Apr 20, 2018 at 4:16 PM, Dan McDonald <
[hidden email]> wrote:

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

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