Wada-H
commented
3 years ago Hi, Andrew
Thank you for your report of this issue. I will check this point, and inform you as soon as possible.
Housei
Open agclark12 opened 3 years ago
Wada-H
commented
3 years ago Hi, Andrew
Thank you for your report of this issue. I will check this point, and inform you as soon as possible.
Housei
Wada-H
commented
3 years ago Please let me know a little more information. What are the image types? *The image should be an 8-bit and 16-bit hyperstack in C, Z.
Wada-H
commented
3 years ago Sorry again and again. C, Z doesn't matter, but if it's a single image, checking the direction to XY will work. But this problem seems to be caused by the fact that the necessary data is not stored in the getFlattenedImage(). So let's explore why this is happening.
Wada-H
commented
3 years ago It would be helpful if you could tell me the message at CheckMesh, since the error message may be different between CheckMesh and Flattened Image. Furthermore, if ChecMesh doesn't work, inevitably FlattenedImage won't work either. Also, I forgot to mention that the error is not considered to be from javafx. If it's from javafx, it's because there is something wrong with the plugin's startup.
agclark12
commented
3 years ago Hi Housei,
Thanks for getting back to me on this. The images are ok I think. The are single channel z-stacks. The plugin converts them to hyperstacks when it starts running. I think the reason I was getting the above message was because I was not getting CheckMesh to work before running FlattenedImage. I can replicate this error if I just click FlattenedImage without doing CheckMesh first. Part of the trouble came from the fact that I consistently get the error below when I run CheckMesh. Naively, I thought that I could ignore this and run FlattenedImage anyway, but I guess not, since CheckMesh MUST be run first (sorry for not reading the ReadMe closely enough before...). It turns out that I always get this error when running CheckMesh, but if I close the log and run CheckMesh again, it always works the second time. I see this on two separate machines, one running OSX, the other a newer windows machine. So for me, it's fine, I know that I always have to run CheckMesh twice. I don't know what's causing the error when it runs the first time or if other users see the same.
Exception in thread "Run$_JavaFX Application Thread" java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1774)
at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1657)
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.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.Node.fireEvent(Node.java:8411)
at javafx.scene.control.Button.fire(Button.java:185)
at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:182)
at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:96)
at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:89)
at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
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.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$MouseHandler.process(Scene.java:3757)
at javafx.scene.Scene$MouseHandler.access$1500(Scene.java:3485)
at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1762)
at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2494)
at com.sun.javafx.tk.quantum.EmbeddedScene.lambda$null$4(EmbeddedScene.java:256)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.tk.quantum.EmbeddedScene.lambda$mouseEvent$5(EmbeddedScene.java:244)
at com.sun.javafx.application.PlatformImpl.lambda$null$5(PlatformImpl.java:295)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.application.PlatformImpl.lambda$runLater$6(PlatformImpl.java:294)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)
Caused by: java.lang.reflect.InvocationTargetException
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 sun.reflect.misc.Trampoline.invoke(MethodUtil.java:71)
at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sun.reflect.misc.MethodUtil.invoke(MethodUtil.java:275)
at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1771)
... 44 more
Caused by: java.lang.OutOfMemoryError
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:598)
at java.util.concurrent.ForkJoinTask.reportException(ForkJoinTask.java:677)
at java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:735)
at java.util.stream.ForEachOps$ForEachOp.evaluateParallel(ForEachOps.java:160)
at java.util.stream.ForEachOps$ForEachOp$OfInt.evaluateParallel(ForEachOps.java:189)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
at java.util.stream.IntPipeline.forEach(IntPipeline.java:405)
at java.util.stream.IntPipeline$Head.forEach(IntPipeline.java:562)
at hw.sheetmeshprojection.MeshManager.createInterpolatedMapForCol(MeshManager.java:120)
at hw.sheetmeshprojection.MeshManager.createInterporatedMap(MeshManager.java:37)
at hw.sheetmeshprojection.SheetMeshProjectionUI.checkMesh(SheetMeshProjectionUI.java:1248)
... 54 more
Caused by: java.lang.OutOfMemoryError: Requested array size exceeds VM limit
HuangLinBao
commented
3 years ago Hi everyone... I've stumbled upon this exception in JavaFX when I only changed the names of the controller and FXML files...everything was working fine until me changing the file names and this exception happened
Exception in Application start method
java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:464)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:363)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at java.base/sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:1051)
Caused by: java.lang.RuntimeException: Exception in Application start method
at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:900)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(LauncherImpl.java:195)
at java.base/java.lang.Thread.run(Thread.java:832)
Caused by: java.lang.IllegalStateException: Location is not set.
at javafx.fxml/javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2541)
at javafx.fxml/javafx.fxml.FXMLLoader.load(FXMLLoader.java:2517)
at org.PCI/org.PCI.App.loadFXML(App.java:33)
at org.PCI/org.PCI.App.start(App.java:20)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:846)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:455)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:428)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:391)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:427)
at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
at javafx.graphics/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at javafx.graphics/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
... 1 more
Exception running application org.PCI.App
I have no idea what happened because everything is set to the new names
Wada-H
commented
3 years ago Thank you for the comments!
Hi Andrew,
In the environments I've studied, the same error probably occurs immediately after performing "Load Roi". This did not happen with 1.52s, but it does happen after 1.53c. I have no idea why it happens, so I have been unable to investigate. It's not a wise choice, but I'm thinking about avoiding this problem by including a process that runs CheckMesh again when CheckMesh fails. Until then, please do it twice to avoid the problem. * I'm worried about shifting to the z direction twice because of this process.
Hi taiq-sabri,
I'm not sure I understand, but does your point mean that the renaming will produce this error in JavaFX regardless of this program?
HuangLinBao
commented
3 years ago well the exception disappeared and the code worked well once I get the original FXML(primary.fxml) and Controller(PrimaryController) names once again..the thing is this exact line in the stack trace made me realize all this exception happened due to me changing the names.
Caused by: java.lang.IllegalStateException: Location is not set.
is there anything we should do if we changed the fxml name on IntelliJ??
Wada-H
commented
3 years ago Hi Andrew,
I have checked the code since then. I have found the cause of the problem, but it does not seem to be solved immediately. (I don't know why the error is happening.) I also checked that CheckMesh works twice, but this method does not give me the results I expect. However, I did find another way to guarantee the results: pressing the Apply switch In this case, the Z checkboxes can be either. It's an extra step, but it's a workaround for now.
Translated with www.DeepL.com/Translator (free version)
Wada-H
commented
3 years ago Hi,
The reason for this is that when the mesh is moved taking into account the thickness value set during "CheckMesh", a calculation is performed to find the intersection point between line segments. It turns out that infinity is sometimes returned when parallel lines appear at this time. I have solved this problem by including a description to avoid this. The modified version will be uploaded to the Fiji update site and the lab website soon.
agclark12
commented
3 years ago Hi Housei. Thanks for looking into this. I look for then new version through the Fiji update site. It's been working fine with the little workaround in the meantime. Thanks again!
best, Andrew
Hi,
I'm trying to use this plugin and have run into some issues with JavaFX. I found this thread on forum.image.fc where you discuss this. I downloaded the OSX JRE8 bundle and installed in FIJI. That allowed me to run the plugin, but I'm now having JavaFX trouble when I click "Check Mesh" or "Flattened Image". The stack trace is below. Thanks very much. I'm looking forward to using this plugin, as it seems to be just what I need to make flattened surface image from my image stacks. Cheers, Andrew