Using User Plugins in Eclipse

[Becksfort, Jared]

Hello,

I cannot figure out how to use a plugin in the plugins folder using the Java API.

For example, I am able to open nifti images using nifti_io from ImageJ, and I check the recorder and it tells me to do this basically:

ImagePlus inImg = IJ.openImage(inFilename); // inFilename ends in .nii, so it should be using Nifti_Reader

But this code fails with

Exception in thread "main" java.lang.NullPointerException
        at ij.Menus.getPlugInsPath(Menus.java:1161)
        at ij.plugin.ClassChecker.getPathsAndNames(ClassChecker.java:68)
        at ij.plugin.ClassChecker.deleteDuplicates(ClassChecker.java:19)
        at ij.plugin.ClassChecker.run(ClassChecker.java:14)
        at ij.IJ.runPlugInUnchecked(IJ.java:175)
        at ij.IJ.runPlugIn(IJ.java:157)
        at ij.IJ.runPlugIn(IJ.java:143)
        at ij.IJ.runUserPlugIn(IJ.java:184)
        at ij.IJ.runPlugIn(IJ.java:154)
        at ij.IJ.runPlugIn(IJ.java:143)
        at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:412)
        at ij.io.Opener.openImage(Opener.java:289)
        at ij.io.Opener.openImage(Opener.java:308)
        at ij.IJ.openImage(IJ.java:1409)
        at utility.PreProcessor.main(PreProcessor.java:31)

I have tried a number of different things to resolve this, such as setting VM arguments -Dplugins.dir and -Dmacros.dir to the directory above plugins as mentioned in the docs.  I am using the Eclipse IDE.  I am trying to use nifti_io (or any other jar in the plugins directory) in Java code and can't seem to get it to work.

Thanks so much to anyone who can help,
Jared

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[dscho]

Hi Jared,

On Sun, 14 Apr 2013, Becksfort, Jared wrote:

> I cannot figure out how to use a plugin in the plugins folder using the
> Java API.

Due to the architecture, this is a non-trivial problem. If you are trying
to debug a plugin without third-party dependencies, you can use the trick
described here:

        http://fiji.sc/Debugging#Debugging_plugins_in_an_IDE_.28Netbeans.2C_IntelliJ.2C_Eclipse.2C_etc.29

For the record, Fiji's Debug class is designed to adjust settings so that
you can run ImageJ inside, say, Eclipse:

https://github.com/fiji/fiji/blob/master/src-plugins/fiji-lib/src/main/java/fiji/Debug.java

If you are uncomfortable with adding fiji-lib as a dependency to your
project, feel free to replicate everything from that class.

Ciao,
Johannes

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[Becksfort, Jared]

Johannes,

Thank you very much for the quick and helpful response.  I have not tried it yet but am more optimistic now that it will work.  If I have more trouble I will post another message.

Jared

-----Original Message-----
From: Johannes Schindelin [mailto:[hidden email]]
Sent: Sunday, April 14, 2013 4:29 PM
To: Becksfort, Jared
Cc: [hidden email]
Subject: Re: Using User Plugins in Eclipse

Hi Jared,

On Sun, 14 Apr 2013, Becksfort, Jared wrote:

> I cannot figure out how to use a plugin in the plugins folder using
> the Java API.

Due to the architecture, this is a non-trivial problem. If you are trying to debug a plugin without third-party dependencies, you can use the trick described here:

        http://fiji.sc/Debugging#Debugging_plugins_in_an_IDE_.28Netbeans.2C_IntelliJ.2C_Eclipse.2C_etc.29

For the record, Fiji's Debug class is designed to adjust settings so that you can run ImageJ inside, say, Eclipse:

https://github.com/fiji/fiji/blob/master/src-plugins/fiji-lib/src/main/java/fiji/Debug.java

If you are uncomfortable with adding fiji-lib as a dependency to your project, feel free to replicate everything from that class.

Ciao,
Johannes


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