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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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Bio-Formats Exporter can deadlock on OS X #2238

Open ctrueden opened 8 years ago

ctrueden commented 8 years ago

When attempting to reproduce #2237 on OS X, the Bio-Formats Exporter dialog never appears on my OS X 10.11 system. Instead, I get a deadlock:

Found one Java-level deadlock:
=============================
"Bio-Formats Exporter":
  waiting to lock monitor 0x000000011a806048 (object 0x00000006444d46d8, a java.lang.Object),
  which is held by "AWT-EventQueue-0"
"AWT-EventQueue-0":
  waiting to lock monitor 0x000000011a804e68 (object 0x000000066aa10ff8, a java.awt.Component$AWTTreeLock),
  which is held by "Bio-Formats Exporter"

Java stack information for the threads listed above:
===================================================
"Bio-Formats Exporter":
    at com.apple.laf.AquaFileSystemModel.getRowCount(AquaFileSystemModel.java:194)
    - waiting to lock <0x00000006444d46d8> (a java.lang.Object)
    at javax.swing.JTable.getRowCount(JTable.java:2662)
    at javax.swing.plaf.basic.BasicTableUI.createTableSize(BasicTableUI.java:1692)
    at javax.swing.plaf.basic.BasicTableUI.getPreferredSize(BasicTableUI.java:1733)
    at javax.swing.JComponent.getPreferredSize(JComponent.java:1661)
    at javax.swing.ScrollPaneLayout.preferredLayoutSize(ScrollPaneLayout.java:495)
    at java.awt.Container.preferredSize(Container.java:1788)
    - locked <0x000000066aa10ff8> (a java.awt.Component$AWTTreeLock)
    at java.awt.Container.getPreferredSize(Container.java:1773)
    at javax.swing.JComponent.getPreferredSize(JComponent.java:1663)
    at java.awt.BorderLayout.preferredLayoutSize(BorderLayout.java:719)
    - locked <0x000000066aa10ff8> (a java.awt.Component$AWTTreeLock)
    at java.awt.Container.preferredSize(Container.java:1788)
    - locked <0x000000066aa10ff8> (a java.awt.Component$AWTTreeLock)
    at java.awt.Container.getPreferredSize(Container.java:1773)
    at javax.swing.JComponent.getPreferredSize(JComponent.java:1663)
    at java.awt.BorderLayout.preferredLayoutSize(BorderLayout.java:719)
    - locked <0x000000066aa10ff8> (a java.awt.Component$AWTTreeLock)
    at java.awt.Container.preferredSize(Container.java:1788)
    - locked <0x000000066aa10ff8> (a java.awt.Component$AWTTreeLock)
    at java.awt.Container.getPreferredSize(Container.java:1773)
    at javax.swing.JComponent.getPreferredSize(JComponent.java:1663)
    at javax.swing.BoxLayout.checkRequests(BoxLayout.java:483)
    at javax.swing.BoxLayout.layoutContainer(BoxLayout.java:424)
    - locked <0x0000000644741298> (a javax.swing.BoxLayout)
    at java.awt.Container.layout(Container.java:1503)
    at java.awt.Container.doLayout(Container.java:1492)
    at java.awt.Container.validateTree(Container.java:1688)
    at java.awt.Container.validateTree(Container.java:1697)
    at java.awt.Container.validateTree(Container.java:1697)
    at java.awt.Container.validateTree(Container.java:1697)
    at java.awt.Container.validateTree(Container.java:1697)
    at java.awt.Container.validate(Container.java:1623)
    - locked <0x000000066aa10ff8> (a java.awt.Component$AWTTreeLock)
    at java.awt.Container.validateUnconditionally(Container.java:1660)
    - locked <0x000000066aa10ff8> (a java.awt.Component$AWTTreeLock)
    at java.awt.Window.pack(Window.java:818)
    at javax.swing.JFileChooser.createDialog(JFileChooser.java:805)
    at javax.swing.JFileChooser.showDialog(JFileChooser.java:732)
    at javax.swing.JFileChooser.showSaveDialog(JFileChooser.java:664)
    at loci.plugins.out.Exporter.run(Exporter.java:236)
    at loci.plugins.LociExporter.run(LociExporter.java:75)
    at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)
    at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:112)
    at ij.IJ.runUserPlugIn(IJ.java:214)
    at ij.IJ.runPlugIn(IJ.java:176)
    at ij.Executer.runCommand(Executer.java:136)
    at ij.Executer.run(Executer.java:65)
    at java.lang.Thread.run(Thread.java:745)
"AWT-EventQueue-0":
    at java.awt.Component.invalidate(Component.java:2920)
    - waiting to lock <0x000000066aa10ff8> (a java.awt.Component$AWTTreeLock)
    at java.awt.Container.invalidate(Container.java:1580)
    at javax.swing.JComponent.revalidate(JComponent.java:4862)
    at javax.swing.JTable.tableRowsInserted(JTable.java:4482)
    at javax.swing.JTable.tableChanged(JTable.java:4407)
    at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:296)
    at javax.swing.table.AbstractTableModel.fireTableRowsInserted(AbstractTableModel.java:231)
    at com.apple.laf.AquaFileSystemModel$DoChangeContents.run(AquaFileSystemModel.java:458)
    - locked <0x00000006444d46d8> (a java.lang.Object)
    - locked <0x000000063fc952f0> (a java.lang.Object)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:745)
    at java.awt.EventQueue.access$300(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:706)
    at java.awt.EventQueue$3.run(EventQueue.java:704)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:715)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

Happens with Oracle Java 1.7.0_80 as well as Oracle Java 1.8.0_66. And it happens with both the release and 5.1 dev versions of Bio-Formats.

ctrueden commented 8 years ago

It seems odd that FileChooser#showSaveDialog deadlocks when called off the EDT on OS X, but I guess the fix could be to wrap that call in EventQueue.invokeAndWait...

bramalingam commented 8 years ago

Thank you for submitting the issue Curtis. The same was reproducible locally, and a card has been created on this regard. https://trello.com/c/L7dtKWsl/96-bio-format-exporter-issues

ctrueden commented 8 years ago

Thanks @bramalingam !

joshmoore commented 8 years ago

Closing in favor of the card. Thanks, guys.

dgault commented 4 years ago

Reopening thsi issue as new reports of the same issue have been received in https://forum.image.sc/t/trouble-with-bio-formats-exporter-in-fiji-macos/41820

The user setup for the new reports is: macOS 10.14.6 (Mojave) ImageJ 2.1.0/1.53c; Java 1.8.0_202 [x86_64] Bio-Formats Plugins for ImageJ Release 6.5.1

imagesc-bot commented 4 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/trouble-with-bio-formats-exporter-in-fiji-macos/41820/4

imagesc-bot commented 3 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/problem-with-bio-format-exporter/58192/2

dgault commented 2 years ago

Further reports of this issue of imagesc - https://forum.image.sc/t/problem-with-bio-format-exporter/58192/2 The post includes some sceanrios for reproducing the issue and details of the user system

dgault commented 2 years ago

Another report of this, also on MacOS Mojave: https://forum.image.sc/t/export-image-sequence-as-avi-and-bio-formats/67199

imagesc-bot commented 2 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/export-image-sequence-as-avi-and-bio-formats/67199/5