Exception when setting point colors/classifications in v0.4.1 #1202
Comments
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Thanks @OpenScienceProject I can replicate the problem. The issue comes from how the icon colors are set; ultimately, it's connected to some changes that were made to overcome some awkward JavaFX/ControlsFX behavior that was making the icon colors wrong in dark mode. I'll look into it, but I suspect a new release will be needed to have an effective workaround.
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Since you're building from source anyway, commenting out the line 275 - The exception is really mysterious though, since it's complaining about a value being bound immediately after it has been explicitly unbound... so I'm really not sure yet what's going on. Setting the color simply sets the |
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Actually, ignore that last suggestion... change line 375 of Using textFillProperty().bind(glyph.textFillProperty());instead of textFillProperty().bindBidirectional(glyph.textFillProperty());seems to fix the issue, but I need to check it doesn't have some other undesirable effect. |
petebankhead
changed the title
Fixes * qupath#1202 * qupath#1203 Also fix minor typo.
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I've just compiled QuPath from main and can confirm that this bug has now been fixed (in 0.4.1, setting a point annotation class causes a "bidirectional binding failed error"). Thanks Pete! |
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Brilliant, thanks @zindy! Very reassuring to have any fixes validated, I hope v0.4.2 can last longer than v0.4.0 and v0.4.1 :) |
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The fix worked for me too. |
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v0.4.2 is now available so I'll close this |
Describe the bug
On QuPath 0.4.1, when I try to create points, at the moment I right click to set a Class, the bug appears, and a log window indicates:
INFO: QuPath build: Version: 0.4.1 Build time: 2023-01-07, 12:00 INFO: Setting tile cache size to 3972.00 MB (25.0% max memory) INFO: Refreshing extensions in Path/to/QuPath/extensions/extensions INFO: Added extension: Path/to/QuPath/extensions/extensions/qupath-extension-stardist-0.4.0.jar INFO: Added extension: Path/to/QuPath/extensions/extensions/qupath-extension-cellpose-0.6.0.jar INFO: Added extension: Path/to/QuPath/extensions/extensions/qupath-extension-imagecombiner-0.2.3.jar INFO: Initializing type adapters INFO: CUDA detected and will be used if possible. Use DnnTools.setUseCuda(false) to turn this off. INFO: Loaded extension BIOP Cellpose extension (3 ms) INFO: Bio-Formats version 6.11.1 INFO: Bio-Formats memoization is turned OFF (based on Java 17.0.5+8, Bio-Formats 6.11.1) INFO: Loaded extension Bio-Formats options (Bio-Formats 6.11.1) (9 ms) INFO: Loaded extension ImageCombiner extension (1 ms) INFO: Loaded extension ImageJ extension (34 ms) INFO: Loaded extension Processing extension (16 ms) INFO: Loaded extension Rich script editor extension (144 ms) INFO: Loaded extension SVG export extension (0 ms) INFO: Loaded extension StarDist extension (2 ms) INFO: OpenSlide version 3.4.1 INFO: Starting QuPath with parameters: [] INFO: Update check for https://github.com/qupath/qupath INFO: No newer release for QuPath (0.4.1 is newer than 0.4.1) INFO: Update check for https://github.com/qupath/qupath-extension-stardist INFO: No newer release for StarDist extension (0.4.0 is newer than 0.4.0) INFO: Update check for https://github.com/biop/qupath-extension-cellpose INFO: No newer release for Cellpose 2D QuPath Extension (0.6.0 is newer than 0.6.0) WARN: Selecting project file /media/image_in/T7 Shield/Recherche/LABO/12.22-Efferocytose_InCuCyte/qupath/QupathProject_donneur1/project.qpproj INFO: Project set to Project: QupathProject_donneur1-project INFO: Setting max Bio-Formats readers to 20 WARN: Removing alpha channel ... (a lot of warnings) WARN: Removing alpha channel ERROR: QuPath exception: Bidirectional binding failed, setting to the previous value java.lang.RuntimeException: Bidirectional binding failed, setting to the previous value at com.sun.javafx.binding.BidirectionalBinding$TypedGenericBidirectionalBinding.invalidated(BidirectionalBinding.java:677) at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:136) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80) at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:106) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113) at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147) at javafx.css.StyleableObjectProperty.set(StyleableObjectProperty.java:82) at javafx.scene.control.Labeled.setTextFill(Labeled.java:766) at org.controlsfx.glyphfont.Glyph.setColor(Glyph.java:288) at qupath.lib.gui.tools.IconFactory.createROIIcon(IconFactory.java:275) at qupath.lib.gui.tools.IconFactory.createPathObjectIcon(IconFactory.java:228) at qupath.lib.gui.tools.PathObjectLabels$PathObjectMiniPane.setPathObject(PathObjectLabels.java:253) at qupath.lib.gui.tools.PathObjectLabels$PathObjectTreeCell.updateItem(PathObjectLabels.java:126) at qupath.lib.gui.tools.PathObjectLabels$PathObjectTreeCell.updateItem(PathObjectLabels.java:113) at javafx.scene.control.TreeCell.updateItem(TreeCell.java:533) at javafx.scene.control.TreeCell.lambda$new$3(TreeCell.java:173) at javafx.beans.WeakInvalidationListener.invalidated(WeakInvalidationListener.java:83) at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:348) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80) at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:106) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113) at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147) at javafx.scene.control.TreeView.setRoot(TreeView.java:479) at qupath.lib.gui.panes.PathObjectHierarchyView.setImageData(PathObjectHierarchyView.java:424) at qupath.lib.gui.panes.PathObjectHierarchyView.changed(PathObjectHierarchyView.java:446) at qupath.lib.gui.panes.PathObjectHierarchyView.changed(PathObjectHierarchyView.java:64) at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:360) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80) at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:106) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113) at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147) at qupath.lib.gui.QuPathGUI.fireImageDataChangedEvent(QuPathGUI.java:4538) at qupath.lib.gui.QuPathGUI$MultiviewManager.imageDataChanged(QuPathGUI.java:5077) at qupath.lib.gui.viewer.QuPathViewer.fireImageDataChanged(QuPathViewer.java:1695) at qupath.lib.gui.viewer.QuPathViewer.setImageData(QuPathViewer.java:1596) at qupath.lib.gui.QuPathGUI.openImageEntry(QuPathGUI.java:2992) at qupath.lib.gui.panes.ProjectBrowser.lambda$new$4(ProjectBrowser.java:201) 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.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:3599) at javafx.scene.Scene$MouseHandler.process(Scene.java:3903) at javafx.scene.Scene.processMouseEvent(Scene.java:1887) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2620) 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(Unknown Source) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449) at com.sun.glass.ui.View.handleMouseEvent(View.java:551) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(GtkApplication.java:316) at java.base/java.lang.Thread.run(Unknown Source) Caused by DuplicatableGlyph.textFill : A bound value cannot be set. at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:143) at javafx.css.StyleableObjectProperty.set(StyleableObjectProperty.java:82) at javafx.beans.property.ObjectProperty.setValue(ObjectProperty.java:78) at com.sun.javafx.binding.BidirectionalBinding$TypedGenericBidirectionalBinding.invalidated(BidirectionalBinding.java:650) at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:136) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80) at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:106) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113) at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147) at javafx.css.StyleableObjectProperty.set(StyleableObjectProperty.java:82) at javafx.scene.control.Labeled.setTextFill(Labeled.java:766) at org.controlsfx.glyphfont.Glyph.setColor(Glyph.java:288) at qupath.lib.gui.tools.IconFactory.createROIIcon(IconFactory.java:275) at qupath.lib.gui.tools.IconFactory.createPathObjectIcon(IconFactory.java:228) at qupath.lib.gui.tools.PathObjectLabels$PathObjectMiniPane.setPathObject(PathObjectLabels.java:253) at qupath.lib.gui.tools.PathObjectLabels$PathObjectTreeCell.updateItem(PathObjectLabels.java:126) at qupath.lib.gui.tools.PathObjectLabels$PathObjectTreeCell.updateItem(PathObjectLabels.java:113) at javafx.scene.control.TreeCell.updateItem(TreeCell.java:533) at javafx.scene.control.TreeCell.lambda$new$3(TreeCell.java:173) at javafx.beans.WeakInvalidationListener.invalidated(WeakInvalidationListener.java:83) at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:348) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80) at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:106) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113) at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147) at javafx.scene.control.TreeView.setRoot(TreeView.java:479) at qupath.lib.gui.panes.PathObjectHierarchyView.setImageData(PathObjectHierarchyView.java:424) at qupath.lib.gui.panes.PathObjectHierarchyView.changed(PathObjectHierarchyView.java:446) at qupath.lib.gui.panes.PathObjectHierarchyView.changed(PathObjectHierarchyView.java:64) at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:360) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80) at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:106) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:113) at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:147) at qupath.lib.gui.QuPathGUI.fireImageDataChangedEvent(QuPathGUI.java:4538) at qupath.lib.gui.QuPathGUI$MultiviewManager.imageDataChanged(QuPathGUI.java:5077) at qupath.lib.gui.viewer.QuPathViewer.fireImageDataChanged(QuPathViewer.java:1695) at qupath.lib.gui.viewer.QuPathViewer.setImageData(QuPathViewer.java:1596) at qupath.lib.gui.QuPathGUI.openImageEntry(QuPathGUI.java:2992) at qupath.lib.gui.panes.ProjectBrowser.lambda$new$4(ProjectBrowser.java:201) 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.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:3599) at javafx.scene.Scene$MouseHandler.process(Scene.java:3903) at javafx.scene.Scene.processMouseEvent(Scene.java:1887) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2620) 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(Unknown Source) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449) at com.sun.glass.ui.View.handleMouseEvent(View.java:551) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(GtkApplication.java:316) at java.base/java.lang.Thread.run(Unknown Source) INFO: Image data set to ImageData: Brightfield (other), Training Img (Classifier) ERROR: Bidirectional binding failed, setting to the previous value (see full stack trace above, or use 'debug' log level) ERROR: Bidirectional binding failed, setting to the previous value (see full stack trace above, or use 'debug' log level)When I run it on QuPath 0.4.0, I don't have this issue.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
Unable to set Class to points.
Screenshots
Desktop (please complete the following information):
Additional context
It is a version of QuPath build on source to be compatible with Cuda for Gpu acceleration (for CellPose).
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