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| // Note: This sets the class according to spot/cluster location, | |
| // but does not try to set meaningful colors at this point | |
| // Get all spots/clusters | |
| def clusters = getObjects({p -> p.class == qupath.imagej.detect.cells.SubcellularDetection.SubcellularObject.class}) | |
| // Loop through all clusters | |
| for (c in clusters) { | |
| // Find the containing cell | |
| def cell = c.getParent() | |
| // Check the current classification - remove the last part if it | |
| // was generated by a previous run of this command | |
| def pathClass = c.getPathClass() | |
| if (["Nuclear", "Cytoplasmic"].contains(c.getName())) { | |
| pathClass = pathClass.getParentClass() | |
| } | |
| // Check the location of the cluster centroid relative to the nucleus, | |
| // and classify accordingly | |
| def nucleus = cell.getNucleusROI() | |
| if (nucleus != null && nucleus.contains(c.getROI().getCentroidX(), c.getROI().getCentroidY())) { | |
| c.setPathClass(getDerivedPathClass(c.getPathClass(), "Nuclear")) | |
| } else | |
| c.setPathClass(getDerivedPathClass(c.getPathClass(), "Cytoplasmic")) | |
| } | |
| fireHierarchyUpdate() |
Hi Pete,
I have used the following code for nuclear-particle detection, and received the following error. If you want to have a look at it. Thanks.
ERROR: Error at line 5: No signature of method: org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.getObjects() is applicable for argument types: (Script3$_run_closure1) values: [Script3$_run_closure1@473bacd0]
ERROR: Script error
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.callGlobal(GroovyScriptEngineImpl.java:399)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.access$100(GroovyScriptEngineImpl.java:90)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl$3.invokeMethod(GroovyScriptEngineImpl.java:303)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl$3.invokeMethod(GroovyScriptEngineImpl.java:292)
at groovy.lang.GroovyObjectSupport.invokeMethod(GroovyObjectSupport.java:44)
at groovy.lang.Script.invokeMethod(Script.java:77)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:70)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:168)
at Script3.run(Script3.groovy:5)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:317)
at org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.eval(GroovyScriptEngineImpl.java:155)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:766)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:696)
at qupath.lib.gui.scripting.DefaultScriptEditor.executeScript(DefaultScriptEditor.java:676)
at qupath.lib.gui.scripting.DefaultScriptEditor$2.run(DefaultScriptEditor.java:1033)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
@ranadeyuq My guess is that in the script editor, the option Run → Include default bindings isn't selected.
In general, these gists are kind of 'throwaway' scripts to answer a specific question. This one would have been written for QuPath v0.1.2 but won't necessarily work in v0.2.0 because some pretty major changes are being made. The really important scripts should become built-in features of the software eventually, so that they can be kept up-to-date with changing versions.
Thanks!