Java.lang.null Error

image

Hi all, I recently began working with TMA slides and have de-arrayed all the slides, saved, ran the positive pixel detection and saved the data and then shut my computer down. However, now when I try to open the images, the session is not responding and after several minutes QuPath shows the error pictured. This error doesn’t appear when trying to open all of the images in the project, but only the ones which were analyzed. I was wondering if anyone could possibly help me determine the issue.

Thanks!

I am guessing that your script ran into problems, either with max memory or there not being any positive pixels. Are you running version 0.1.2? Did you test the script on the images one by one?
This thread might be useful: https://groups.google.com/d/msg/qupath-users/PpGsVcm0U4c/qTlFIYD8BgAJ

Another possibility is that your data files may be too big. I have run into that before too with very “fine” settings on very large tissue samples. I think there is around a 4GB limit? Though I forget exactly.

To make an educated guess what could be the problem, I’d need to know

  • The version of QuPath you’re using (the same one now as for the analysis, right?)
  • A more complete error message, which should hopefully be available under View → Show log

I ran analysis in v0.2.0-m2, but the program was unresponsive when I would click to access the script editor under Automate even when I would close out of the session and re-start. So I re-downloaded the same version (v0.2.0-m2) and deleted the old one thinking that it could be some issue since I tinkered with the source code, but the program was still unresponsive when I tried to open the script editor. Then I remembered having a similar issue a while back and Reset preferences and it started to work again, but now I couldn’t access some of the images and TMA grids which I had created with the version I had deleted despite it being the same version of QuPath. I had read your warning about switching between versions but I interpreted that to mean to be careful as projects may not open correctly between versions (e.g. v0.2.0-m2 vs. v0.1.2 or 0.1.3), and not specific downloads of the same version.

This is a more complete error log.

WARN: Openslide: Property 'openslide.level[0].tile-width' not available, will return default value 256.0
WARN: Openslide: Property 'openslide.level[0].tile-height' not available, will return default value 256.0
INFO: Test reading thumbnail with openslide: passed (BufferedImage@7d1336aa: type = 1 DirectColorModel: rmask=ff0000 gmask=ff00 bmask=ff amask=0 IntegerInterleavedRaster: width = 117 height = 200 #Bands = 3 xOff = 0 yOff = 0 dataOffset[0] 0)
INFO: Returning server: OpenSlide for file:/M:/6_12_2019_LPR_DAB_TMA/AT8-DAB-5_29_19_11.06.2019_11.13.13.mrxs
ERROR: Reached end of file...
ERROR: Error
    at qupath.lib.objects.hierarchy.PathObjectHierarchy.setHierarchy(PathObjectHierarchy.java:563)
    at qupath.lib.io.PathIO.readImageDataSerialized(PathIO.java:201)
    at qupath.lib.io.PathIO.readImageData(PathIO.java:276)
    at qupath.lib.projects.DefaultProject$DefaultProjectImageEntry.readImageData(DefaultProject.java:763)
    at qupath.lib.gui.QuPathGUI.openImageEntry(QuPathGUI.java:2293)
    at qupath.lib.gui.panels.ProjectBrowser.lambda$new$2(ProjectBrowser.java:170)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    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.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.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$ClickGenerator.postProcess(Scene.java:3564)
    at javafx.scene.Scene$ClickGenerator.access$8200(Scene.java:3492)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3860)
    at javafx.scene.Scene$MouseHandler.access$1200(Scene.java:3579)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1849)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2588)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:397)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:434)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:390)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:433)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at com.sun.glass.ui.View.notifyMouse(View.java:942)
    at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
    at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
    at java.base/java.lang.Thread.run(Thread.java:834)
ERROR: Load ImageData: QuPath has encountered a problem, sorry.
If you can replicate it, please notify a developer.

java.lang.NullPointerException

That’s a good thought, but after resetting preferences, I always make sure to increase the allotted memory for QuPath to 10GB, apply and close out of the current session before opening a new one with those settings. Additionally, I am running these analyses on v0.2.0-m2.

Unfortunately, I cannot test the images one by one as some will not even open.

I’m afraid it looks like the .qpdata file is incomplete. This has been reported a couple of times, but not very often and I don’t think anyone has been able to find a way to reproduce it consistently.

My guess is that if the project is on a network drive then there might be some connection issue causing the problem. Could that be the case for you?

For more information, see

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