java exception error when using lsm toolbox

[Pengyao Jiang]

Hi there,

I have been using lsm toolbox plugin to batch convert lsm files to tif
files without any problem. I'm using version 1.48v, 64bit version in linux.
However, today when I open pluin/ lsm toolbox, select batch convert and
select the directory that contains all the lsm files, it did not display
any lsm files in the directory and throws errors as following:

Exception occurred during event dispatching:
java.lang.NullPointerException
at
org.imagearchive.lsm.toolbox.gui.BatchDialog.processPath(BatchDialog.java:245)
at
org.imagearchive.lsm.toolbox.gui.BatchDialog.processPath(BatchDialog.java:242)
at
org.imagearchive.lsm.toolbox.gui.BatchDialog$3.actionPerformed(BatchDialog.java:196)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.Component.processMouseEvent(Component.java:6289)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6054)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4652)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4482)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4482)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:603)
at java.awt.EventQueue$1.run(EventQueue.java:601)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:617)
at java.awt.EventQueue$2.run(EventQueue.java:615)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:178)
at java.awt.Dialog$1.run(Dialog.java:1046)
at java.awt.Dialog$3.run(Dialog.java:1098)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Dialog.show(Dialog.java:1096)
at java.awt.Component.show(Component.java:1585)
at java.awt.Component.setVisible(Component.java:1537)
at java.awt.Window.setVisible(Window.java:842)
at java.awt.Dialog.setVisible(Dialog.java:986)
at
org.imagearchive.lsm.toolbox.gui.ControlPanelFrame$5.actionPerformed(ControlPanelFrame.java:320)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
at java.awt.Component.processMouseEvent(Component.java:6289)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6054)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4652)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4482)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4482)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:603)
at java.awt.EventQueue$1.run(EventQueue.java:601)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:617)
at java.awt.EventQueue$2.run(EventQueue.java:615)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)



The same kind of error shows up when I use fiji. Does anyone know what the
problem is and how to fix this? Thank you so much!!!


--
Best,
Pengyao Jiang
University of Chicago
Ecology & Evolution

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jerome Mutterer-3]

For the record, this was worked around using the following macro that
allows splitting folders of LSM files.

https://gist.github.com/mutterer/a7ab071d06348798b382

Sincerely,

Jerome


On 20 April 2015 at 21:08, Pengyao Jiang <[hidden email]> wrote:

> Hi there,
>
> I have been using lsm toolbox plugin to batch convert lsm files to tif
> files without any problem. I'm using version 1.48v, 64bit version in linux.
> However, today when I open pluin/ lsm toolbox, select batch convert and
> select the directory that contains all the lsm files, it did not display
> any lsm files in the directory and throws errors as following:
>
> Exception occurred during event dispatching:
> java.lang.NullPointerException
> at
>
> org.imagearchive.lsm.toolbox.gui.BatchDialog.processPath(BatchDialog.java:245)
> at
>
> org.imagearchive.lsm.toolbox.gui.BatchDialog.processPath(BatchDialog.java:242)
> at
>
> org.imagearchive.lsm.toolbox.gui.BatchDialog$3.actionPerformed(BatchDialog.java:196)
> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
> at
>
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
> at
>
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
> at
>
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
> at java.awt.Component.processMouseEvent(Component.java:6289)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
> at java.awt.Component.processEvent(Component.java:6054)
> at java.awt.Container.processEvent(Container.java:2041)
> at java.awt.Component.dispatchEventImpl(Component.java:4652)
> at java.awt.Container.dispatchEventImpl(Container.java:2099)
> at java.awt.Component.dispatchEvent(Component.java:4482)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
> at java.awt.Container.dispatchEventImpl(Container.java:2085)
> at java.awt.Window.dispatchEventImpl(Window.java:2478)
> at java.awt.Component.dispatchEvent(Component.java:4482)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
> at java.awt.EventQueue.access$000(EventQueue.java:85)
> at java.awt.EventQueue$1.run(EventQueue.java:603)
> at java.awt.EventQueue$1.run(EventQueue.java:601)
> at java.security.AccessController.doPrivileged(Native Method)
> at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
> at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
> at java.awt.EventQueue$2.run(EventQueue.java:617)
> at java.awt.EventQueue$2.run(EventQueue.java:615)
> at java.security.AccessController.doPrivileged(Native Method)
> at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
> at
>
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
> at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
> at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:178)
> at java.awt.Dialog$1.run(Dialog.java:1046)
> at java.awt.Dialog$3.run(Dialog.java:1098)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.awt.Dialog.show(Dialog.java:1096)
> at java.awt.Component.show(Component.java:1585)
> at java.awt.Component.setVisible(Component.java:1537)
> at java.awt.Window.setVisible(Window.java:842)
> at java.awt.Dialog.setVisible(Dialog.java:986)
> at
>
> org.imagearchive.lsm.toolbox.gui.ControlPanelFrame$5.actionPerformed(ControlPanelFrame.java:320)
> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
> at
>
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
> at
>
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
> at
>
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
> at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
> at java.awt.Component.processMouseEvent(Component.java:6289)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
> at java.awt.Component.processEvent(Component.java:6054)
> at java.awt.Container.processEvent(Container.java:2041)
> at java.awt.Component.dispatchEventImpl(Component.java:4652)
> at java.awt.Container.dispatchEventImpl(Container.java:2099)
> at java.awt.Component.dispatchEvent(Component.java:4482)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
> at java.awt.Container.dispatchEventImpl(Container.java:2085)
> at java.awt.Window.dispatchEventImpl(Window.java:2478)
> at java.awt.Component.dispatchEvent(Component.java:4482)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
> at java.awt.EventQueue.access$000(EventQueue.java:85)
> at java.awt.EventQueue$1.run(EventQueue.java:603)
> at java.awt.EventQueue$1.run(EventQueue.java:601)
> at java.security.AccessController.doPrivileged(Native Method)
> at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
> at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
> at java.awt.EventQueue$2.run(EventQueue.java:617)
> at java.awt.EventQueue$2.run(EventQueue.java:615)
> at java.security.AccessController.doPrivileged(Native Method)
> at
>
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
> at
>
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
> at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
> at
>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>
>
>
> The same kind of error shows up when I use fiji. Does anyone know what the
> problem is and how to fix this? Thank you so much!!!
>
>
> --
> Best,
> Pengyao Jiang
> University of Chicago
> Ecology & Evolution
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Jerome Mutterer
CNRS - Institut de biologie moléculaire des plantes
12, rue du Général Zimmer
67084 Strasbourg Cedex
www.ibmp.cnrs.fr

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html