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qupath / qupath-extension-instanseg

The official QuPath extension for InstanSeg
https://github.com/instanseg/instanseg
Apache License 2.0
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Select all TMA cores in InstanSeg runs on missing cores #105

Closed lauracmurphy closed 1 week ago

lauracmurphy commented 1 week ago

Problem I'm assuming is unintended behaviour

Opening the InstanSeg GUI while a TMA is open helpfully gives an option to run for all TMA cores, however, it ignores if the cores as classed as valid or missing.

Solution

Don't run InstanSeg on the 'Missing' cores.

alanocallaghan commented 1 week ago

Fair point

petebankhead commented 1 week ago

Related-ish - should selection also be added to the command history (both for annotations and TMA cores)?

I have the feeling it probably should, since otherwise we'll need to be telling people to add a line to their script anyway if they want to do batch processing.

petebankhead commented 1 week ago

Actually, another (more related) issue is that trying to select cores when there aren't any results in an exception:

17:38:36.13 [JavaFX Application Thread] ERROR   qupath.lib.gui.QuPathUncaughtExceptionHandler   java.lang.reflect.InvocationTargetException java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1863)
    at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1731)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
    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.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:49)
    at javafx.event.Event.fireEvent(Event.java:199)
    at javafx.scene.Node.fireEvent(Node.java:8963)
    at javafx.scene.control.ToggleButton.fire(ToggleButton.java:263)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:207)
    at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:199)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3987)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1893)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2711)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301)
    at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:430)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:560)
    at com.sun.glass.ui.View.notifyMouse(View.java:946)
    at com.sun.glass.ui.mac.MacView.notifyMouse(MacView.java:128)
Caused by: java.lang.reflect.InvocationTargetException
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:115)
    at java.base/java.lang.reflect.Method.invoke(Method.java:580)
    at com.sun.javafx.reflect.Trampoline.invoke(MethodUtil.java:72)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
    at java.base/java.lang.reflect.Method.invoke(Method.java:580)
    at com.sun.javafx.reflect.MethodUtil.invoke(MethodUtil.java:270)
    at com.sun.javafx.fxml.MethodHelper.invoke(MethodHelper.java:84)
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1860)
    ... 52 more
Caused by: java.lang.NullPointerException: Cannot invoke "qupath.lib.objects.hierarchy.TMAGrid.getTMACoreList()" because the return value of "qupath.lib.objects.hierarchy.PathObjectHierarchy.getTMAGrid()" is null
    at qupath.ext.instanseg.ui.InstanSegController.selectAllTMACores(InstanSegController.java:848)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
    ... 59 more

Using the same approach as QP.selectTMACores should resolve that I think.

alanocallaghan commented 1 week ago

Well, at least the relevant exception is in there somewhere. Will address in a moment unless you want to

petebankhead commented 1 week ago

Go for it, I'm looking at why my attempts to pass parameters brings down the VM...