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morphonets / SNT

The ImageJ framework for quantification of neuronal anatomy
https://imagej.net/plugins/snt
GNU General Public License v3.0
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Sciview: java.lang.NoClassDefFoundError: sc/iview/vector/Vector3 #51

Closed tferr closed 2 years ago

tferr commented 3 years ago

newer versions of sciview no longer have Vector3. We need to modernize SciViewSNT @kephale , @skalarproduktraum , what is the proper replacement for Vector3?

Currently, this is what happens if one tries to sync SNT contents into sciview: Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: sc/iview/vector/Vector3

Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: sc/iview/vector/Vector3 at sc.fiji.snt.SciViewSNT.add(SciViewSNT.java:237) at sc.fiji.snt.SciViewSNT.syncPathManagerList(SciViewSNT.java:275) at sc.fiji.snt.SNTUI.lambda$sciViewerPanel$35(SNTUI.java:1748) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289) at java.awt.Component.processMouseEvent(Component.java:6539) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6304) at java.awt.Container.processEvent(Container.java:2239) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2297) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476) at java.awt.Container.dispatchEventImpl(Container.java:2283) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84) at java.awt.EventQueue$4.run(EventQueue.java:733) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:730) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.ClassNotFoundException: sc.iview.vector.Vector3 at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 40 more Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: sc/iview/vector/Vector3 at sc.fiji.snt.SciViewSNT.add(SciViewSNT.java:237) at sc.fiji.snt.SciViewSNT.syncPathManagerList(SciViewSNT.java:275) at sc.fiji.snt.SNTUI.lambda$sciViewerPanel$35(SNTUI.java:1748) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289) at java.awt.Component.processMouseEvent(Component.java:6539) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6304) at java.awt.Container.processEvent(Container.java:2239) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2297) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476) at java.awt.Container.dispatchEventImpl(Container.java:2283) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84) at java.awt.EventQueue$4.run(EventQueue.java:733) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:730) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: java.lang.ClassNotFoundException: sc.iview.vector.Vector3 at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 40 more
kephale commented 3 years ago

org.joml.Vector3f (and org.joml.Vector4f for 4d)

We gave up on maintaining a Vector layer because it led to too many unnecessary copies. It is fairly painless to change and I'll put it onto my Todo, but it will be a few days-week before I can dig in.

kephale commented 3 years ago

BTW is there a test class that I can use instead of going through the UI each time?

tferr commented 3 years ago

The only tests we have are these ones: https://github.com/morphonets/SNT/tree/master/src/test/java/sc/fiji/snt :disappointed:

tferr commented 3 years ago

@kephale , does this help at all? https://github.com/morphonets/SNT/blob/master/src/main/resources/script_templates/Neuroanatomy/Render/SciView_Demo.groovy

kephale commented 3 years ago

yes <3

tferr commented 2 years ago

This seems to be now fixed with #80