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knime-ip / knip-ilastik

KNIP / Ilastik Integration (BETA)
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ArrayIndexOutOfBoundsException with 3D data #7

Closed imagejan closed 7 years ago

imagejan commented 7 years ago

I get an ArrayIndexOutOfBoundsException from ImgWriter2 when trying to use the Ilastik Headless node with 3D data.

Here's an example workflow: Ilastik Tests.zip

and a very simple Ilastik project that I used (please unzip): knip-ilastik-tests.zip

This is the exception from knime.log:

java.lang.ArrayIndexOutOfBoundsException: 3
    at net.imglib2.AbstractInterval.dimension(AbstractInterval.java:243)
    at net.imglib2.AbstractWrappedInterval.dimension(AbstractWrappedInterval.java:59)
    at net.imagej.ImgPlus.dimension(ImgPlus.java:220)
    at net.imglib2.AbstractWrappedInterval.dimension(AbstractWrappedInterval.java:59)
    at net.imglib2.AbstractWrappedInterval.dimension(AbstractWrappedInterval.java:59)
    at net.imagej.ImgPlus.dimension(ImgPlus.java:220)
    at org.knime.knip.io.nodes.imgwriter2.ImgWriter2.writeImage(ImgWriter2.java:280)
    at org.knime.knip.io.nodes.imgwriter2.ImgWriter2.writeImage(ImgWriter2.java:231)
    at org.knime.knip.ilastik.nodes.headless.IlastikHeadlessNodeModel.execute(IlastikHeadlessNodeModel.java:241)
    at org.knime.core.node.NodeModel.execute(NodeModel.java:732)
    at org.knime.core.node.NodeModel.executeModel(NodeModel.java:566)
    at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1146)
    at org.knime.core.node.Node.execute(Node.java:933)
    at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:556)
    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)
imagejan commented 7 years ago

The version served by the nightly build update site is still serving 0.2.2.v201607220824. Is this fix already available to end users somewhere?

dietzc commented 7 years ago

I will try to cut a nightly build release today.