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Diozao666 opened this issue Aug 14, 2024 · 0 comments
Open

marrow quant script error #6

Diozao666 opened this issue Aug 14, 2024 · 0 comments

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@Diozao666
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Hello
I am trying to run the MarroQuant script and I am getting this:

ERROR: Error at line 70: null

ERROR: Script error
    at qupath.imagej.objects.ROIConverterIJ.convertToPathROI(ROIConverterIJ.java:222)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite$StaticMetaMethodSiteNoUnwrap.invoke(StaticMetaMethodSite.java:133)
    at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.call(StaticMetaMethodSite.java:91)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at MarrowQuant.getQuPathPathObject(Script19.groovy:528)
    at MarrowQuant$getQuPathPathObject$3.callCurrent(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
    at MarrowQuant.sendResultsToQuPath(Script19.groovy:427)
    at MarrowQuant.run(Script19.groovy:187)
    at MarrowQuant$run.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
    at Script19$_run_closure2.doCall(Script19.groovy:83)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
    at groovy.lang.Closure.call(Closure.java:414)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.eachWithIndex(DefaultGroovyMethods.java:1956)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.eachWithIndex(DefaultGroovyMethods.java:1936)
    at org.codehaus.groovy.runtime.DefaultGroovyMethods.eachWithIndex(DefaultGroovyMethods.java:1986)
    at org.codehaus.groovy.runtime.dgm$175.invoke(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
    at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at Script19.run(Script19.groovy:71)
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:317)
    at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:155)
    at qupath.lib.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:767)
    at qupath.lib.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:697)
    at qupath.lib.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:679)
    at qupath.lib.scripting.DefaultScriptEditor.access$400(DefaultScriptEditor.java:138)
    at qupath.lib.scripting.DefaultScriptEditor$2.run(DefaultScriptEditor.java:1034)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

I thought it had to do with some measured areas which the perimeter was not possible to calculate (N/A), but the error was the same. Another thing that might be interfering with it is that the Tissue Boundaries area is being set just as "Area" instead of "Area (AWT)" like in the tutorial. Any idea of what I am doing wrong?

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