Cell Density Map

Research_Associate · February 22, 2021, 10:37pm

Nice update! Missed when the multi selection happened.

As I recall Jet is a “legacy” colormap and is kind of it’s own thing. I recall trying to do some terrible coding and Jet was the ONLY colormap I could figure out how to use at first.

Running into errors with composite classes:
ERROR: QuPath exception: Cannot invoke method getParentClass() on null object
Steps:

create 2 single measurement classifiers
create a composite from the two
classify cells
Select complex classification from dropdown

log

ERROR: QuPath exception: Cannot invoke method getParentClass() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:44)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:34)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
at Script1$_DensityMap_closure4.doCall(Script1.groovy:36)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1029)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.BooleanReturningMethodInvoker.invoke(BooleanReturningMethodInvoker.java:49)
at org.codehaus.groovy.runtime.callsite.BooleanClosureWrapper.call(BooleanClosureWrapper.java:52)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4914)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4786)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.findAll(DefaultGroovyMethods.java:4771)
at org.codehaus.groovy.runtime.dgm$242.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:247)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at Script1.DensityMap(Script1.groovy:36)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:351)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
at Script1$_MakeSubMenu_closure6$_closure9$_closure10.doCall(Script1.groovy:140)
at jdk.internal.reflect.GeneratedMethodAccessor13.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1029)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:428)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2318)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2303)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2344)
at org.codehaus.groovy.runtime.dgm$200.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:247)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at Script1$_MakeSubMenu_closure6$_closure9.doCall(Script1.groovy:127)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1029)
at groovy.lang.Closure.call(Closure.java:412)
at org.codehaus.groovy.runtime.ConvertedClosure.invokeCustom(ConvertedClosure.java:50)
at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:110)
at com.sun.proxy.$Proxy30.handle(Unknown Source)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
at javafx.event.Event.fireEvent(Event.java:198)
at javafx.scene.control.MenuItem.fire(MenuItem.java:459)
at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1380)
at com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(ContextMenuContent.java:1333)
at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
at javafx.event.Event.fireEvent(Event.java:198)
at javafx.scene.Scene$MouseHandler.process(Scene.java:3890)
at javafx.scene.Scene.processMouseEvent(Scene.java:1885)
at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2618)
at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409)
at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447)
at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412)
at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446)
at com.sun.glass.ui.View.handleMouseEvent(View.java:556)
at com.sun.glass.ui.View.notifyMouse(View.java:942)
at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
at java.base/java.lang.Thread.run(Unknown Source)

Will look into it when I get a chance.

EP.Zindy · February 22, 2021, 11:02pm

Hello @Research_Associate,

Nice update! Missed when the multi selection happened.

Sorry, I thought people were getting bored of seeing that thread at the top of the list every time I made some updates, so I ninja-edited my code and the text that goes with. I did document the changes though!

Thank you for looking into this when you get a chance. I’m still learning QuPath and haven’t had a chance to combine classifiers the way you describe

We’ll get there… eventually!

Research_Associate · February 22, 2021, 11:26pm

I haven’t had a chance to fully error check it, but I adjusted the contextMenu around line 200 to:

    contextMenu.setOnShowing((event) -> {
    //logger.info(gui.getViewers().size().toString())
    //logger.info(viewer.hasServer().toString())
        if(gui.getViewers().size() >1){
            classNames = ["Positive","Negative"]+QuPathGUI.getInstance().getAvailablePathClasses()*.toString()
            classNames.unique()
        }else if(viewer.hasServer()){
            objectsToCheck = getQuPath().getImageData()?.getHierarchy()?.getDetectionObjects()
            classNames = objectsToCheck.collect{it.getPathClass().toString()}.unique()
        }else{
            classNames = ["Positive","Negative"]+QuPathGUI.getInstance().getAvailablePathClasses()*.toString()
            classNames.unique()
        }
        //Dialogs.showInfoNotification("Custom button", "menu event")
        item1.getItems().clear();
        def classItems = MakeSubMenu(classNames, preferredClassName.get())
        item1.getItems().addAll(classItems)
    });

Now if there is an image open with objects in it, it only uses classes for currently available *detection objects:

Gah, now it throws an error if no image is open, even so. I’ll need to check that, I vaguely remember…

** Perfect, fixed it, should show the entire list when no image is open, or show the list of objects from the currently open image if one image is open. Not sure what happens if multiple images are open…
And after checking, it uses the currently selected viewer, which is I guess the only way I can think of doing it right now…
I suppose if I can check for multiple viewers being open, that could default back to the original full list?

Research_Associate · February 23, 2021, 12:14am

Ok, updated the above a couple of more times, but it now seems to handle multiple viewers, no viewers, or no selected viewers. All with full lists. If one viewer is up and selected, it limits the class list to what is present in that viewer.

And an update to my original concern:


def filteredDetections = detections.findAll {it.getPathClass()?.getParentClass() == pathClass.getParentClass()}

Adding in the one ? prevents the error and allows complex classes.
In this section around line 35

    pathClass = getPathClass(objectClass)
    if (pathClass.getParentClass() == null) {
        positiveDetections = detections.findAll {it.getPathClass() == getPathClass(objectClass)}
    } else {
        positiveDetections = detections.findAll {it.getPathClass() == pathClass}
        def filteredDetections = detections.findAll {it.getPathClass()?.getParentClass() == pathClass.getParentClass()}
        detections = filteredDetections
    }

Sigh, one more thing, on my end I found it far more useful to have a fixed density, so that the colors were meaningful across multiple images rather than having the bright spots mean different things in different images. And yes, I could see how that would vary a bit per image. Not sure if it is worth making them a global variable.