Knime - error after updating using Community Contributions Stable Update Site

knime
Tags: #<Tag:0x00007fd53e2fc5e0>

#1

Dear all,

in Knime I added the Community Contributions Stable Update-Site, following https://tech.knime.org/wiki/install-knime-image-processing
After installation I am getting an error using the Median Filter or Global Thresholder-node:

Execute failed: net.imagej.ops.create.CreateNamespace.img(Lnet/imglib2/Interval;Lnet/imglib2/type/Type;)Lnet/imglib2/img/Img;

Same workflow was working before the update.

Is there something wrong in my settings?
Thanks
Anna


#2

Does that mean that you had another version of KNIME Image Processing before, e.g. from the “KNIME Community Contributions (3.3)” (trusted/3.3), or from the “nightly builds” update site?
Could it be that you have some version skew now?

It would be helpful if you can report the versions of the different KNIME Image Processing modules in your installation as reported by Help > Installed Software, also possibly also the exact error from your knime.log (inside .metadata/knime/ in your workspace).

I’m sure that @dietzc or @gab1one will be able to advise then.


As a workaround, you can try to make a new KNIME installation and point it to the same workspace.


#3

Thank you for your help! I took the information below from the installation history and the knime.log:

Before:
KNIME Image Processing 1.4.1.201511190728
KNIME Image Processing - OMERO Integration 0.10.0.201510111033

After:
KNIME Image Processing 1.4.1.201512010705
KNIME Image Processing - CellProfiler Integration 0.2.0.201510252145
KNIME Image Processing - Clear Volume Integration 0.1.0.201510270800
KNIME Image Processing - Ilastik Integration 0.1.1.201510281448
KNIME Image Processing - ImageJ 3D Viewer Integration 1.1.0.201510111042
KNIME Image Processing - ImageJ Integration (Beta) 0.10.0.201510230800
KNIME Image Processing - OMERO Integration 0.10.0.201510111033
KNIME Image Processing - Python Extensions 1.0.0.201510221600
KNIME Image Processing - Tess4J Integration 1.2.0.201510252148

The knime.log tells me this:

2017-03-14 09:24:34,594 : ERROR : KNIME-Worker-6 : Median Filter : Median Filter : 0:5 : Execute failed: net.imagej.ops.create.CreateNamespace.img(Lnet/imglib2/Interval;Lnet/imglib2/type/Type;)Lnet/imglib2/img/Img;
2017-03-14 09:24:34,594 : DEBUG : KNIME-Worker-6 : Median Filter : Median Filter : 0:5 : Execute failed: net.imagej.ops.create.CreateNamespace.img(Lnet/imglib2/Interval;Lnet/imglib2/type/Type;)Lnet/imglib2/img/Img;
java.lang.NoSuchMethodError: net.imagej.ops.create.CreateNamespace.img(Lnet/imglib2/Interval;Lnet/imglib2/type/Type;)Lnet/imglib2/img/Img;
	at org.knime.knip.core.util.ImgPlusFactory.instantiate(ImgPlusFactory.java:76)
	at org.knime.knip.core.util.ImgPlusFactory.instantiate(ImgPlusFactory.java:1)
	at org.knime.knip.base.node.ImgPlusToImgPlusNodeModel.compute(ImgPlusToImgPlusNodeModel.java:176)
	at org.knime.knip.base.node.ImgPlusToImgPlusNodeModel.compute(ImgPlusToImgPlusNodeModel.java:1)
	at org.knime.knip.base.node.ValueToCellNodeModel$1.getCells(ValueToCellNodeModel.java:376)
	at org.knime.knip.base.node.ValueToCellNodeModel.execute(ValueToCellNodeModel.java:525)
	at org.knime.core.node.NodeModel.executeModel(NodeModel.java:563)
	at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1136)
	at org.knime.core.node.Node.execute(Node.java:932)
	at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:554)
	at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:95)
	at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:179)
	at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:110)
	at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:328)
	at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:204)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
	at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)

#4

I re-installed KNIME and the Image Processing Community Contributions + Additional Image Processing Plugings and it is now working. (Just playing with the ImageJ-macro node, very cool…) Thank you again.


#5

Hi @aklemm,

Great that you got it working (thanks @imagejan)!! Let me know if you need anything else. You can also visit http://knime.imagej.net/, where you can find tons of KNIP example workflows and more information on the project.

Cheers,

Christian


#6

Hi Christian,

yes, it’s great :slight_smile:, thanks . In general, is it better to post KNIME-related imaging questions in the ImageJ-Forum or in the KNIME-forum?

Cheers,
Anna


#7

Hi Anna,

oh, this is really up to you. Whatever you prefer :thumbsup:!

Best,

Christian