[ImageJ-devel] SCIFIO and imageJ1

[Pietro Incardona]

Hi Curtis

I already strongly suggest to use Fiji/ImageJ2, but I would like (if 
reasonably possible) to maintain an imageJ version

I packed this in the jar file

/imglib2-2.0.0-beta-26.jar
/imglib2-2.0.0-SNAPSHOT.jar
/imglib2-algorithms-2.0.0-beta-26.jar
/imglib2-algorithms-gpl-2.0.0-beta-26.jar
/imglib2-algorithms-legacy-2.0.0-beta-26.jar
/imglib2-ij-2.0.0-beta-26.jar
/imglib2-meta-2.0.0-beta-26.jar
/imglib2-ops-2.0.0-beta-26.jar
/imglib2-realtransform-2.0.0-beta-26.jar
/imglib2-ui-2.0.0-SNAPSHOT.jar
/scifio-0.16.5.jar
/scifio-bf-compat-1.8.4.jar
/scifio-cli-0.1.0.jar
/scifio-jai-imageio-1.1.0.jar
/scifio-lifesci-0.5.2.jar
/scifio-ome-xml-0.9.2.jar
/scifio-tools-0.14.0.jar
/scijava-common-2.33.0.jar
/scijava-plugins-commands-0.1.7.jar
/scijava-plugins-platforms-0.1.2.jar
/scijava-plugins-text-markdown-0.1.1.jar
/scijava-plugins-text-plain-0.1.1.jar
/scijava-ui-awt-0.1.2.jar
/scijava-ui-swing-0.3.0.jar


Apparently it crashes on the instruction

         // create the ImgOpener
         ImgOpener imgOpener = new ImgOpener();

ImageJ 1.48v; Java 1.6.0_24 [64-bit]; Linux 3.16.3-200.fc20.x86_64; 10MB 
of 455MB (2%)

java.lang.IllegalArgumentException: No compatible service: 
io.scif.SCIFIOService
     at 
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:242)
     at 
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:193)
     at 
org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:169)
     at org.scijava.Context.<init>(Context.java:234)
     at org.scijava.Context.<init>(Context.java:195)
     at org.scijava.Context.<init>(Context.java:138)
     at org.scijava.Context.<init>(Context.java:126)
     at 
io.scif.img.AbstractImgIOComponent.<init>(AbstractImgIOComponent.java:57)
     at io.scif.img.ImgOpener.<init>(ImgOpener.java:94)
     at mosaic.core.utils.MosaicTest.processResult(MosaicTest.java:178)
     at mosaic.core.utils.MosaicTest.testPlugin(MosaicTest.java:335)
     at mosaic.plugins.test.Jtest.naturalization(Jtest.java:32)
     at mosaic.plugins.Jtest.setup(Jtest.java:39)
     at 
ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:47)
     at ij.IJ.runUserPlugIn(IJ.java:201)
     at ij.IJ.runPlugIn(IJ.java:163)
     at ij.Executer.runCommand(Executer.java:131)
     at ij.Executer.run(Executer.java:64)
     at java.lang.Thread.run(Thread.java:662)


Cheers
Pietro

On 01/14/2015 05:07 PM, Curtis Rueden wrote:
> Hi Pietro,
>
> > Is there any way to pack a jar with SCIFIO included that work also in
> > imageJ1
>
> Certainly. But it would help to be more specific about what you are 
> trying to do.
>
> By "pack a jar with SCIFIO" do you mean "create an uber-JAR with 
> dependencies embedded"? Or something else?
>
> By "ImageJ1" do you mean the vanilla ImageJ1 distribution from 
> imagej.nih.gov <http://imagej.nih.gov>? If so, you can do it, but I 
> would recommend saving yourself a lot of work and just recommending 
> people use ImageJ2, which comes with SCIFIO already bundled. But if 
> you really want to go that route, look at the maven-shade-plugin or 
> maven-assembly-plugin [1].
>
> Regards,
> Curtis
>
> [1] Here is a starting point for how we create an ImageJ2 uber-JAR 
> with dependencies: 
> https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-22/pom.xml#L421-L648. 
> Your use case would likely be simpler.
>
> On Wed, Jan 14, 2015 at 7:18 AM, Pietro Incardona <incardon at mpi-cbg.de 
> <mailto:incardon at mpi-cbg.de>> wrote:
>
>     Hi All
>
>     Is there any way to pack a jar with SCIFIO included that work also
>     in imageJ1
>
>     Cheers
>     Pietro
>
>
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>

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