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Please help me with compilating plugins in Eclipse

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GeraldT

Please help me with compilating plugins in Eclipse

Hello everybody,

Since Fiji removed the tools.jar I cannot compile from the editor anymore. So now I am (again) trying to use the Eclipse, JDK combo.
I have managed to import the Fiji source as maven project and run it from Eclipse. I followed the instructions from: http://imagej.net/Developing_ImageJ_in_Eclipse. I am now trying to make a PluginFrame plugin.

This is what I have done:
- created new source folder with the name: MandibularAssymetryMeasure_
- inside that catalog I made two class files:
Main Plugin class:
import ij.*;
import ij.plugin.frame.*;

public class MandibularAssymetryMeasure_ extends PlugInFrame {

private static final long serialVersionUID = 4723432002956229961L;

public MandibularAssymetryMeasure_() {
super("MandibularAssymetryMeasure_");
}

public void run(String arg) {
IJ.log("Hello World!");
}

}
Launcher:
import fiji.Debug;

public class Tester {

public static void main(String[] args) {
Debug.run("MandibularAssymetryMeasure_", null);
}

}

They both reside in the fiji-master folder. And I created the file plugins.config in the fiji-master\resources folder:
# Name: MandibularAssymetryMeasure_
# Author: Gerald Torgersen
# Version: 0.1
# Date: 2016/10/xx
# Requires: ImageJ 1.51f

Plugins>MandibularAssymetryMeasure_, "Run MandibularAssymetryMeasure_", MandibularAssymetryMeasure_("run")

I run the the Tester class as a Java application and it starts Fiji, but I get an error message: Unrecognized command: "MandibularAssymetryMeasure_"

I have not made a special pom-file for that plugin. I do not know how, or where to put it. Please help me somebody. The Norwegian dental health depends on my ImageJ programming ;-)

Mvh
Gerald R. Torgersen
IT-seksjonen,
Det odontologiske fakultet, Universitetet i Oslo
Faculty of Dentistry Universitetet i Oslo, University of Oslo http://www.odont.uio.no/personer/adm/fak/gerald

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

GeraldT

Re: Please help me with compilating plugins in Eclipse

I did it!!!!! After all the years first time it worked!! I only had to use the minimal project (https://github.com/imagej/minimal-ij1-plugin/zipball/master). I did not read down there because I thought the error was earlier in the process. I now used ImageJ and not Fiji source.
There is still a tiny problem: The ImageJ does not close, I get an:
Exception in thread "Quit" java.lang.NullPointerException
at ij.WindowManager.getIDList(WindowManager.java:147)
at ij.ImageJ.run(ImageJ.java:745)
at java.lang.Thread.run(Thread.java:745)

Any advice here? Besides that I am happy, i don't know how many hours I have tried ....

Mvh
Gerald R. Torgersen

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>Gerald Ruiner Torgersen
>Sent: Wednesday, October 26, 2016 2:17 PM
>To: [hidden email]
>Subject: Please help me with compilating plugins in Eclipse
>
>Hello everybody,
>
>Since Fiji removed the tools.jar I cannot compile from the editor anymore. So
>now I am (again) trying to use the Eclipse, JDK combo.
>I have managed to import the Fiji source as maven project and run it from Eclipse.
>I followed the instructions from:
>http://imagej.net/Developing_ImageJ_in_Eclipse. I am now trying to make a
>PluginFrame plugin.
>
>This is what I have done:
>- created new source folder with the name: MandibularAssymetryMeasure_
>- inside that catalog I made two class files:
>Main Plugin class:
>import ij.*;
>import ij.plugin.frame.*;
>
>public class MandibularAssymetryMeasure_ extends PlugInFrame {
>
> private static final long serialVersionUID = 4723432002956229961L;
>
> public MandibularAssymetryMeasure_() {
> super("MandibularAssymetryMeasure_");
> }
>
> public void run(String arg) {
> IJ.log("Hello World!");
> }
>
>}
>Launcher:
>import fiji.Debug;
>
>public class Tester {
>
> public static void main(String[] args) {
> Debug.run("MandibularAssymetryMeasure_", null);
> }
>
>}
>
>They both reside in the fiji-master folder. And I created the file plugins.config in
>the fiji-master\resources folder:
># Name: MandibularAssymetryMeasure_
># Author: Gerald Torgersen
># Version: 0.1
># Date: 2016/10/xx
># Requires: ImageJ 1.51f
>
>Plugins>MandibularAssymetryMeasure_, "Run MandibularAssymetryMeasure_",
>Plugins>MandibularAssymetryMeasure_("run")
>
>I run the the Tester class as a Java application and it starts Fiji, but I get an error
>message: Unrecognized command: "MandibularAssymetryMeasure_"
>
>I have not made a special pom-file for that plugin. I do not know how, or where
>to put it. Please help me somebody. The Norwegian dental health depends on my
>ImageJ programming ;-)
>
>Mvh
>Gerald R. Torgersen
>IT-seksjonen,
>Det odontologiske fakultet, Universitetet i Oslo Faculty of Dentistry Universitetet i
>Oslo, University of Oslo http://www.odont.uio.no/personer/adm/fak/gerald
>
>--
>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

ctrueden

Re: Please help me with compilating plugins in Eclipse

Hi Gerald,

> I did it!!!!! After all the years first time it worked!!

Congratulations!

> Since Fiji removed the tools.jar I cannot compile from the editor
> anymore.

We removed tools.jar (and javac.jar) specifically so that compilation from
the Script Editor _would_ work for the Java-8 version of Fiji, which is the
current version you get when you download from http://fiji.sc/#download.
Did you test with a fresh download? It should work out of the box, as long
as you have a JDK installed on your system.

> Exception in thread "Quit" java.lang.NullPointerException
> at ij.WindowManager.getIDList(WindowManager.java:147)
> at ij.ImageJ.run(ImageJ.java:745)
> at java.lang.Thread.run(Thread.java:745)

Which version of ImageJ 1.x are you using? Is your code on GitHub?

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/

On Wed, Oct 26, 2016 at 9:44 AM, Gerald Ruiner Torgersen <
[hidden email]> wrote:

> I did it!!!!! After all the years first time it worked!! I only had to use
> the minimal project (https://github.com/imagej/min
> imal-ij1-plugin/zipball/master). I did not read down there because I
> thought the error was earlier in the process. I now used ImageJ and not
> Fiji source.
> There is still a tiny problem: The ImageJ does not close, I get an:
> Exception in thread "Quit" java.lang.NullPointerException
> at ij.WindowManager.getIDList(WindowManager.java:147)
> at ij.ImageJ.run(ImageJ.java:745)
> at java.lang.Thread.run(Thread.java:745)
>
> Any advice here? Besides that I am happy, i don't know how many hours I
> have tried ....
>
> Mvh
> Gerald R. Torgersen
>
>
> >-----Original Message-----
> >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> >Gerald Ruiner Torgersen
> >Sent: Wednesday, October 26, 2016 2:17 PM
> >To: [hidden email]
> >Subject: Please help me with compilating plugins in Eclipse
> >
> >Hello everybody,
> >
> >Since Fiji removed the tools.jar I cannot compile from the editor
> anymore. So
> >now I am (again) trying to use the Eclipse, JDK combo.
> >I have managed to import the Fiji source as maven project and run it from
> Eclipse.
> >I followed the instructions from:
> >http://imagej.net/Developing_ImageJ_in_Eclipse. I am now trying to make a
> >PluginFrame plugin.
> >
> >This is what I have done:
> >- created new source folder with the name: MandibularAssymetryMeasure_
> >- inside that catalog I made two class files:
> >Main Plugin class:
> >import ij.*;
> >import ij.plugin.frame.*;
> >
> >public class MandibularAssymetryMeasure_ extends PlugInFrame {
> >
> > private static final long serialVersionUID = 4723432002956229961L;
> >
> > public MandibularAssymetryMeasure_() {
> > super("MandibularAssymetryMeasure_");
> > }
> >
> > public void run(String arg) {
> > IJ.log("Hello World!");
> > }
> >
> >}
> >Launcher:
> >import fiji.Debug;
> >
> >public class Tester {
> >
> > public static void main(String[] args) {
> > Debug.run("MandibularAssymetryMeasure_", null);
> > }
> >
> >}
> >
> >They both reside in the fiji-master folder. And I created the file
> plugins.config in
> >the fiji-master\resources folder:
> ># Name: MandibularAssymetryMeasure_
> ># Author: Gerald Torgersen
> ># Version: 0.1
> ># Date: 2016/10/xx
> ># Requires: ImageJ 1.51f
> >
> >Plugins>MandibularAssymetryMeasure_, "Run MandibularAssymetryMeasure_",
> >Plugins>MandibularAssymetryMeasure_("run")
> >
> >I run the the Tester class as a Java application and it starts Fiji, but
> I get an error
> >message: Unrecognized command: "MandibularAssymetryMeasure_"
> >
> >I have not made a special pom-file for that plugin. I do not know how, or
> where
> >to put it. Please help me somebody. The Norwegian dental health depends
> on my
> >ImageJ programming ;-)
> >
> >Mvh
> >Gerald R. Torgersen
> >IT-seksjonen,
> >Det odontologiske fakultet, Universitetet i Oslo Faculty of Dentistry
> Universitetet i
> >Oslo, University of Oslo http://www.odont.uio.no/personer/adm/fak/gerald
> >
> >--
> >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

GeraldT

Re: Please help me with compilating plugins in Eclipse

Hello Curtis,

Thank you for trying to help me. Actually I have installed/uninstalled the JDK twice, and also downloaded the whole Fiji zip several times and tried to unpack it in several locations. I always got the error message "javac not found" or something like that. Maybe it is just the PC at my work which has problems. But I am more happy using Eclipse which helps me to easy draw GUIs.

The version of ImageJ I am using is the source package I downloaded yesterday, the version is 1.49q. My code is not on Github. I am just making small plugins enabling colleagues to easy mark and measure sites on oral x-rays. But if one of them gets really good maybe i should consider? I am not a real programmer, just a physicist helping on research projects.
Now I am just happy my "Hello world" plugin compiles and starts :-)

The thing is that I have to kill the javaw process in order to stop the ImageJ from running. From the Windows Task Manager.

Mvh
Gerald R. Torgersen

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis
>Rueden
>Sent: Wednesday, October 26, 2016 7:13 PM
>To: [hidden email]
>Subject: Re: Please help me with compilating plugins in Eclipse
>
>Hi Gerald,
>
>> I did it!!!!! After all the years first time it worked!!
>
>Congratulations!
>
>> Since Fiji removed the tools.jar I cannot compile from the editor
>> anymore.
>
>We removed tools.jar (and javac.jar) specifically so that compilation from the
>Script Editor _would_ work for the Java-8 version of Fiji, which is the current
>version you get when you download from http://fiji.sc/#download.
>Did you test with a fresh download? It should work out of the box, as long as you
>have a JDK installed on your system.
>
>> Exception in thread "Quit" java.lang.NullPointerException
>> at ij.WindowManager.getIDList(WindowManager.java:147)
>> at ij.ImageJ.run(ImageJ.java:745)
>> at java.lang.Thread.run(Thread.java:745)
>
>Which version of ImageJ 1.x are you using? Is your code on GitHub?
>
>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/
>
>
>On Wed, Oct 26, 2016 at 9:44 AM, Gerald Ruiner Torgersen <
>[hidden email]> wrote:
>
>> I did it!!!!! After all the years first time it worked!! I only had to
>> use the minimal project (https://github.com/imagej/min
>> imal-ij1-plugin/zipball/master). I did not read down there because I
>> thought the error was earlier in the process. I now used ImageJ and
>> not Fiji source.
>> There is still a tiny problem: The ImageJ does not close, I get an:
>> Exception in thread "Quit" java.lang.NullPointerException
>> at ij.WindowManager.getIDList(WindowManager.java:147)
>> at ij.ImageJ.run(ImageJ.java:745)
>> at java.lang.Thread.run(Thread.java:745)
>>
>> Any advice here? Besides that I am happy, i don't know how many hours
>> I have tried ....
>>
>> Mvh
>> Gerald R. Torgersen
>>
>>
>> >-----Original Message-----
>> >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> >Gerald Ruiner Torgersen
>> >Sent: Wednesday, October 26, 2016 2:17 PM
>> >To: [hidden email]
>> >Subject: Please help me with compilating plugins in Eclipse
>> >
>> >Hello everybody,
>> >
>> >Since Fiji removed the tools.jar I cannot compile from the editor
>> anymore. So
>> >now I am (again) trying to use the Eclipse, JDK combo.
>> >I have managed to import the Fiji source as maven project and run it
>> >from
>> Eclipse.
>> >I followed the instructions from:
>> >http://imagej.net/Developing_ImageJ_in_Eclipse. I am now trying to
>> >make a PluginFrame plugin.
>> >
>> >This is what I have done:
>> >- created new source folder with the name:
>> >MandibularAssymetryMeasure_
>> >- inside that catalog I made two class files:
>> >Main Plugin class:
>> >import ij.*;
>> >import ij.plugin.frame.*;
>> >
>> >public class MandibularAssymetryMeasure_ extends PlugInFrame {
>> >
>> > private static final long serialVersionUID =
>> > 4723432002956229961L;
>> >
>> > public MandibularAssymetryMeasure_() {
>> > super("MandibularAssymetryMeasure_");
>> > }
>> >
>> > public void run(String arg) {
>> > IJ.log("Hello World!");
>> > }
>> >
>> >}
>> >Launcher:
>> >import fiji.Debug;
>> >
>> >public class Tester {
>> >
>> > public static void main(String[] args) {
>> > Debug.run("MandibularAssymetryMeasure_", null);
>> > }
>> >
>> >}
>> >
>> >They both reside in the fiji-master folder. And I created the file
>> plugins.config in
>> >the fiji-master\resources folder:
>> ># Name: MandibularAssymetryMeasure_
>> ># Author: Gerald Torgersen
>> ># Version: 0.1
>> ># Date: 2016/10/xx
>> ># Requires: ImageJ 1.51f
>> >
>> >Plugins>MandibularAssymetryMeasure_, "Run
>> >Plugins>MandibularAssymetryMeasure_",
>> >Plugins>MandibularAssymetryMeasure_("run")
>> >
>> >I run the the Tester class as a Java application and it starts Fiji,
>> >but
>> I get an error
>> >message: Unrecognized command: "MandibularAssymetryMeasure_"
>> >
>> >I have not made a special pom-file for that plugin. I do not know
>> >how, or
>> where
>> >to put it. Please help me somebody. The Norwegian dental health
>> >depends
>> on my
>> >ImageJ programming ;-)
>> >
>> >Mvh
>> >Gerald R. Torgersen
>> >IT-seksjonen,
>> >Det odontologiske fakultet, Universitetet i Oslo Faculty of Dentistry
>> Universitetet i
>> >Oslo, University of Oslo
>> >http://www.odont.uio.no/personer/adm/fak/gerald
>> >
>> >--
>> >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

GeraldT

Re: Please help me with compilating plugins in Eclipse

Hi again, I just discovered the "Terminate" button in Eclipse. And it actually works! It terminates the process running.
This is a great day for me!!!!

Mvh
Gerald R. Torgersen

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>Gerald Ruiner Torgersen
>Sent: Thursday, October 27, 2016 8:45 AM
>To: [hidden email]
>Subject: Re: Please help me with compilating plugins in Eclipse
>
>Hello Curtis,
>
>Thank you for trying to help me. Actually I have installed/uninstalled the JDK
>twice, and also downloaded the whole Fiji zip several times and tried to unpack it
>in several locations. I always got the error message "javac not found" or
>something like that. Maybe it is just the PC at my work which has problems. But I
>am more happy using Eclipse which helps me to easy draw GUIs.
>
>The version of ImageJ I am using is the source package I downloaded yesterday,
>the version is 1.49q. My code is not on Github. I am just making small plugins
>enabling colleagues to easy mark and measure sites on oral x-rays. But if one of
>them gets really good maybe i should consider? I am not a real programmer, just
>a physicist helping on research projects.
>Now I am just happy my "Hello world" plugin compiles and starts :-)
>
>The thing is that I have to kill the javaw process in order to stop the ImageJ from
>running. From the Windows Task Manager.
>
>Mvh
>Gerald R. Torgersen
>
>
>>-----Original Message-----
>>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>>Curtis Rueden
>>Sent: Wednesday, October 26, 2016 7:13 PM
>>To: [hidden email]
>>Subject: Re: Please help me with compilating plugins in Eclipse
>>
>>Hi Gerald,
>>
>>> I did it!!!!! After all the years first time it worked!!
>>
>>Congratulations!
>>
>>> Since Fiji removed the tools.jar I cannot compile from the editor
>>> anymore.
>>
>>We removed tools.jar (and javac.jar) specifically so that compilation
>>from the Script Editor _would_ work for the Java-8 version of Fiji,
>>which is the current version you get when you download from
>http://fiji.sc/#download.
>>Did you test with a fresh download? It should work out of the box, as
>>long as you have a JDK installed on your system.
>>
>>> Exception in thread "Quit" java.lang.NullPointerException
>>> at ij.WindowManager.getIDList(WindowManager.java:147)
>>> at ij.ImageJ.run(ImageJ.java:745)
>>> at java.lang.Thread.run(Thread.java:745)
>>
>>Which version of ImageJ 1.x are you using? Is your code on GitHub?
>>
>>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/
>>
>>
>>On Wed, Oct 26, 2016 at 9:44 AM, Gerald Ruiner Torgersen <
>>[hidden email]> wrote:
>>
>>> I did it!!!!! After all the years first time it worked!! I only had
>>> to use the minimal project (https://github.com/imagej/min
>>> imal-ij1-plugin/zipball/master). I did not read down there because I
>>> thought the error was earlier in the process. I now used ImageJ and
>>> not Fiji source.
>>> There is still a tiny problem: The ImageJ does not close, I get an:
>>> Exception in thread "Quit" java.lang.NullPointerException
>>> at ij.WindowManager.getIDList(WindowManager.java:147)
>>> at ij.ImageJ.run(ImageJ.java:745)
>>> at java.lang.Thread.run(Thread.java:745)
>>>
>>> Any advice here? Besides that I am happy, i don't know how many hours
>>> I have tried ....
>>>
>>> Mvh
>>> Gerald R. Torgersen
>>>
>>>
>>> >-----Original Message-----
>>> >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf
>>> >Of Gerald Ruiner Torgersen
>>> >Sent: Wednesday, October 26, 2016 2:17 PM
>>> >To: [hidden email]
>>> >Subject: Please help me with compilating plugins in Eclipse
>>> >
>>> >Hello everybody,
>>> >
>>> >Since Fiji removed the tools.jar I cannot compile from the editor
>>> anymore. So
>>> >now I am (again) trying to use the Eclipse, JDK combo.
>>> >I have managed to import the Fiji source as maven project and run it
>>> >from
>>> Eclipse.
>>> >I followed the instructions from:
>>> >http://imagej.net/Developing_ImageJ_in_Eclipse. I am now trying to
>>> >make a PluginFrame plugin.
>>> >
>>> >This is what I have done:
>>> >- created new source folder with the name:
>>> >MandibularAssymetryMeasure_
>>> >- inside that catalog I made two class files:
>>> >Main Plugin class:
>>> >import ij.*;
>>> >import ij.plugin.frame.*;
>>> >
>>> >public class MandibularAssymetryMeasure_ extends PlugInFrame {
>>> >
>>> > private static final long serialVersionUID =
>>> > 4723432002956229961L;
>>> >
>>> > public MandibularAssymetryMeasure_() {
>>> > super("MandibularAssymetryMeasure_");
>>> > }
>>> >
>>> > public void run(String arg) {
>>> > IJ.log("Hello World!");
>>> > }
>>> >
>>> >}
>>> >Launcher:
>>> >import fiji.Debug;
>>> >
>>> >public class Tester {
>>> >
>>> > public static void main(String[] args) {
>>> > Debug.run("MandibularAssymetryMeasure_", null);
>>> > }
>>> >
>>> >}
>>> >
>>> >They both reside in the fiji-master folder. And I created the file
>>> plugins.config in
>>> >the fiji-master\resources folder:
>>> ># Name: MandibularAssymetryMeasure_
>>> ># Author: Gerald Torgersen
>>> ># Version: 0.1
>>> ># Date: 2016/10/xx
>>> ># Requires: ImageJ 1.51f
>>> >
>>> >Plugins>MandibularAssymetryMeasure_, "Run
>>> >Plugins>MandibularAssymetryMeasure_",
>>> >Plugins>MandibularAssymetryMeasure_("run")
>>> >
>>> >I run the the Tester class as a Java application and it starts Fiji,
>>> >but
>>> I get an error
>>> >message: Unrecognized command: "MandibularAssymetryMeasure_"
>>> >
>>> >I have not made a special pom-file for that plugin. I do not know
>>> >how, or
>>> where
>>> >to put it. Please help me somebody. The Norwegian dental health
>>> >depends
>>> on my
>>> >ImageJ programming ;-)
>>> >
>>> >Mvh
>>> >Gerald R. Torgersen
>>> >IT-seksjonen,
>>> >Det odontologiske fakultet, Universitetet i Oslo Faculty of
>>> >Dentistry
>>> Universitetet i
>>> >Oslo, University of Oslo
>>> >http://www.odont.uio.no/personer/adm/fak/gerald
>>> >
>>> >--
>>> >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

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

Michael Entrup

Re: Please help me with compilating plugins in Eclipse

In reply to this post by GeraldT

Hi Gerald,

maybe Fiji does not find javac because it is not added to the PATH. If
you use Windows, you can find an instruction at [1]. If you use another
OS, just pick the right one from the list at [2].

Best regards
Michael

[1]:
https://docs.oracle.com/javase/8/docs/technotes/guides/install/windows_jdk_install.html#BABGDJFH
[2]:
https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html

On 27.10.2016 08:44, Gerald Ruiner Torgersen wrote:

> Hello Curtis,
>
> Thank you for trying to help me. Actually I have installed/uninstalled the JDK twice, and also downloaded the whole Fiji zip several times and tried to unpack it in several locations. I always got the error message "javac not found" or something like that. Maybe it is just the PC at my work which has problems. But I am more happy using Eclipse which helps me to easy draw GUIs.
>
> The version of ImageJ I am using is the source package I downloaded yesterday, the version is 1.49q. My code is not on Github. I am just making small plugins enabling colleagues to easy mark and measure sites on oral x-rays. But if one of them gets really good maybe i should consider? I am not a real programmer, just a physicist helping on research projects.
> Now I am just happy my "Hello world" plugin compiles and starts :-)
>
> The thing is that I have to kill the javaw process in order to stop the ImageJ from running. From the Windows Task Manager.
>
> Mvh
> Gerald R. Torgersen
>
>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis
>> Rueden
>> Sent: Wednesday, October 26, 2016 7:13 PM
>> To: [hidden email]
>> Subject: Re: Please help me with compilating plugins in Eclipse
>>
>> Hi Gerald,
>>
>>> I did it!!!!! After all the years first time it worked!!
>>
>> Congratulations!
>>
>>> Since Fiji removed the tools.jar I cannot compile from the editor
>>> anymore.
>>
>> We removed tools.jar (and javac.jar) specifically so that compilation from the
>> Script Editor _would_ work for the Java-8 version of Fiji, which is the current
>> version you get when you download from http://fiji.sc/#download.
>> Did you test with a fresh download? It should work out of the box, as long as you
>> have a JDK installed on your system.
>>
>>> Exception in thread "Quit" java.lang.NullPointerException
>>> at ij.WindowManager.getIDList(WindowManager.java:147)
>>> at ij.ImageJ.run(ImageJ.java:745)
>>> at java.lang.Thread.run(Thread.java:745)
>>
>> Which version of ImageJ 1.x are you using? Is your code on GitHub?
>>
>> 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/
>>
>>
>> On Wed, Oct 26, 2016 at 9:44 AM, Gerald Ruiner Torgersen <
>> [hidden email]> wrote:
>>
>>> I did it!!!!! After all the years first time it worked!! I only had to
>>> use the minimal project (https://github.com/imagej/min
>>> imal-ij1-plugin/zipball/master). I did not read down there because I
>>> thought the error was earlier in the process. I now used ImageJ and
>>> not Fiji source.
>>> There is still a tiny problem: The ImageJ does not close, I get an:
>>> Exception in thread "Quit" java.lang.NullPointerException
>>> at ij.WindowManager.getIDList(WindowManager.java:147)
>>> at ij.ImageJ.run(ImageJ.java:745)
>>> at java.lang.Thread.run(Thread.java:745)
>>>
>>> Any advice here? Besides that I am happy, i don't know how many hours
>>> I have tried ....
>>>
>>> Mvh
>>> Gerald R. Torgersen
>>>
>>>
>>>> -----Original Message-----
>>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>>>> Gerald Ruiner Torgersen
>>>> Sent: Wednesday, October 26, 2016 2:17 PM
>>>> To: [hidden email]
>>>> Subject: Please help me with compilating plugins in Eclipse
>>>>
>>>> Hello everybody,
>>>>
>>>> Since Fiji removed the tools.jar I cannot compile from the editor
>>> anymore. So
>>>> now I am (again) trying to use the Eclipse, JDK combo.
>>>> I have managed to import the Fiji source as maven project and run it
>>>> from
>>> Eclipse.
>>>> I followed the instructions from:
>>>> http://imagej.net/Developing_ImageJ_in_Eclipse. I am now trying to
>>>> make a PluginFrame plugin.
>>>>
>>>> This is what I have done:
>>>> - created new source folder with the name:
>>>> MandibularAssymetryMeasure_
>>>> - inside that catalog I made two class files:
>>>> Main Plugin class:
>>>> import ij.*;
>>>> import ij.plugin.frame.*;
>>>>
>>>> public class MandibularAssymetryMeasure_ extends PlugInFrame {
>>>>
>>>> private static final long serialVersionUID =
>>>> 4723432002956229961L;
>>>>
>>>> public MandibularAssymetryMeasure_() {
>>>> super("MandibularAssymetryMeasure_");
>>>> }
>>>>
>>>> public void run(String arg) {
>>>> IJ.log("Hello World!");
>>>> }
>>>>
>>>> }
>>>> Launcher:
>>>> import fiji.Debug;
>>>>
>>>> public class Tester {
>>>>
>>>> public static void main(String[] args) {
>>>> Debug.run("MandibularAssymetryMeasure_", null);
>>>> }
>>>>
>>>> }
>>>>
>>>> They both reside in the fiji-master folder. And I created the file
>>> plugins.config in
>>>> the fiji-master\resources folder:
>>>> # Name: MandibularAssymetryMeasure_
>>>> # Author: Gerald Torgersen
>>>> # Version: 0.1
>>>> # Date: 2016/10/xx
>>>> # Requires: ImageJ 1.51f
>>>>
>>>> Plugins>MandibularAssymetryMeasure_, "Run
>>>> Plugins>MandibularAssymetryMeasure_",
>>>> Plugins>MandibularAssymetryMeasure_("run")
>>>>
>>>> I run the the Tester class as a Java application and it starts Fiji,
>>>> but
>>> I get an error
>>>> message: Unrecognized command: "MandibularAssymetryMeasure_"
>>>>
>>>> I have not made a special pom-file for that plugin. I do not know
>>>> how, or
>>> where
>>>> to put it. Please help me somebody. The Norwegian dental health
>>>> depends
>>> on my
>>>> ImageJ programming ;-)
>>>>
>>>> Mvh
>>>> Gerald R. Torgersen
>>>> IT-seksjonen,
>>>> Det odontologiske fakultet, Universitetet i Oslo Faculty of Dentistry
>>> Universitetet i
>>>> Oslo, University of Oslo
>>>> http://www.odont.uio.no/personer/adm/fak/gerald
>>>>
>>>> --
>>>> 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
>

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

GeraldT

Re: Please help me with compilating plugins in Eclipse

Hi Michael,

Thank you for your suggestion. The javac.exe is in the path. So the problem is somewhere else. But now Eclipse is working perfectly with Image and I am totally happy :-) This is even better, much better than the script editor.

Greetings Gerald

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Entrup
Sent: 27. oktober 2016 12:58
To: [hidden email]
Subject: Re: Please help me with compilating plugins in Eclipse

Hi Gerald,

maybe Fiji does not find javac because it is not added to the PATH. If you use Windows, you can find an instruction at [1]. If you use another OS, just pick the right one from the list at [2].

Best regards
Michael

[1]:
https://docs.oracle.com/javase/8/docs/technotes/guides/install/windows_jdk_install.html#BABGDJFH
[2]:
https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html

On 27.10.2016 08:44, Gerald Ruiner Torgersen wrote:

> Hello Curtis,
>
> Thank you for trying to help me. Actually I have installed/uninstalled the JDK twice, and also downloaded the whole Fiji zip several times and tried to unpack it in several locations. I always got the error message "javac not found" or something like that. Maybe it is just the PC at my work which has problems. But I am more happy using Eclipse which helps me to easy draw GUIs.
>
> The version of ImageJ I am using is the source package I downloaded yesterday, the version is 1.49q. My code is not on Github. I am just making small plugins enabling colleagues to easy mark and measure sites on oral x-rays. But if one of them gets really good maybe i should consider? I am not a real programmer, just a physicist helping on research projects.
> Now I am just happy my "Hello world" plugin compiles and starts :-)
>
> The thing is that I have to kill the javaw process in order to stop the ImageJ from running. From the Windows Task Manager.
>
> Mvh
> Gerald R. Torgersen
>
>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> Curtis Rueden
>> Sent: Wednesday, October 26, 2016 7:13 PM
>> To: [hidden email]
>> Subject: Re: Please help me with compilating plugins in Eclipse
>>
>> Hi Gerald,
>>
>>> I did it!!!!! After all the years first time it worked!!
>>
>> Congratulations!
>>
>>> Since Fiji removed the tools.jar I cannot compile from the editor
>>> anymore.
>>
>> We removed tools.jar (and javac.jar) specifically so that compilation
>> from the Script Editor _would_ work for the Java-8 version of Fiji,
>> which is the current version you get when you download from http://fiji.sc/#download.
>> Did you test with a fresh download? It should work out of the box, as
>> long as you have a JDK installed on your system.
>>
>>> Exception in thread "Quit" java.lang.NullPointerException
>>> at ij.WindowManager.getIDList(WindowManager.java:147)
>>> at ij.ImageJ.run(ImageJ.java:745)
>>> at java.lang.Thread.run(Thread.java:745)
>>
>> Which version of ImageJ 1.x are you using? Is your code on GitHub?
>>
>> 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/
>>
>>
>> On Wed, Oct 26, 2016 at 9:44 AM, Gerald Ruiner Torgersen <
>> [hidden email]> wrote:
>>
>>> I did it!!!!! After all the years first time it worked!! I only had
>>> to use the minimal project (https://github.com/imagej/min
>>> imal-ij1-plugin/zipball/master). I did not read down there because I
>>> thought the error was earlier in the process. I now used ImageJ and
>>> not Fiji source.
>>> There is still a tiny problem: The ImageJ does not close, I get an:
>>> Exception in thread "Quit" java.lang.NullPointerException
>>> at ij.WindowManager.getIDList(WindowManager.java:147)
>>> at ij.ImageJ.run(ImageJ.java:745)
>>> at java.lang.Thread.run(Thread.java:745)
>>>
>>> Any advice here? Besides that I am happy, i don't know how many
>>> hours I have tried ....
>>>
>>> Mvh
>>> Gerald R. Torgersen
>>>
>>>
>>>> -----Original Message-----
>>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf
>>>> Of Gerald Ruiner Torgersen
>>>> Sent: Wednesday, October 26, 2016 2:17 PM
>>>> To: [hidden email]
>>>> Subject: Please help me with compilating plugins in Eclipse
>>>>
>>>> Hello everybody,
>>>>
>>>> Since Fiji removed the tools.jar I cannot compile from the editor
>>> anymore. So
>>>> now I am (again) trying to use the Eclipse, JDK combo.
>>>> I have managed to import the Fiji source as maven project and run
>>>> it from
>>> Eclipse.
>>>> I followed the instructions from:
>>>> http://imagej.net/Developing_ImageJ_in_Eclipse. I am now trying to
>>>> make a PluginFrame plugin.
>>>>
>>>> This is what I have done:
>>>> - created new source folder with the name:
>>>> MandibularAssymetryMeasure_
>>>> - inside that catalog I made two class files:
>>>> Main Plugin class:
>>>> import ij.*;
>>>> import ij.plugin.frame.*;
>>>>
>>>> public class MandibularAssymetryMeasure_ extends PlugInFrame {
>>>>
>>>> private static final long serialVersionUID =
>>>> 4723432002956229961L;
>>>>
>>>> public MandibularAssymetryMeasure_() {
>>>> super("MandibularAssymetryMeasure_");
>>>> }
>>>>
>>>> public void run(String arg) {
>>>> IJ.log("Hello World!");
>>>> }
>>>>
>>>> }
>>>> Launcher:
>>>> import fiji.Debug;
>>>>
>>>> public class Tester {
>>>>
>>>> public static void main(String[] args) {
>>>> Debug.run("MandibularAssymetryMeasure_", null);
>>>> }
>>>>
>>>> }
>>>>
>>>> They both reside in the fiji-master folder. And I created the file
>>> plugins.config in
>>>> the fiji-master\resources folder:
>>>> # Name: MandibularAssymetryMeasure_ # Author: Gerald Torgersen #
>>>> Version: 0.1 # Date: 2016/10/xx # Requires: ImageJ 1.51f
>>>>
>>>> Plugins>MandibularAssymetryMeasure_, "Run
>>>> Plugins>MandibularAssymetryMeasure_",
>>>> Plugins>MandibularAssymetryMeasure_("run")
>>>>
>>>> I run the the Tester class as a Java application and it starts
>>>> Fiji, but
>>> I get an error
>>>> message: Unrecognized command: "MandibularAssymetryMeasure_"
>>>>
>>>> I have not made a special pom-file for that plugin. I do not know
>>>> how, or
>>> where
>>>> to put it. Please help me somebody. The Norwegian dental health
>>>> depends
>>> on my
>>>> ImageJ programming ;-)
>>>>
>>>> Mvh
>>>> Gerald R. Torgersen
>>>> IT-seksjonen,
>>>> Det odontologiske fakultet, Universitetet i Oslo Faculty of
>>>> Dentistry
>>> Universitetet i
>>>> Oslo, University of Oslo
>>>> http://www.odont.uio.no/personer/adm/fak/gerald
>>>>
>>>> --
>>>> 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
>

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