[ome-users] Support for (big) Slidescanner scn files
Dominik Lindner (Staff)
d.lindner at dundee.ac.uk
Fri Mar 24 11:31:55 GMT 2017
Hi Sascha,
Sorry, I have to correct myself. The export as jpg,png,tif functionality (Insight, OMERO.web and scripts) is limited
by a setting to avoid out-of-memory errors:
https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/config.html#omero-client-download-as-max-size
The default value is equivalent to a 12k x 12k px image. How big is the image, you were talking about?
However, the button in Insight image viewer is not taking that into account, that's a bug, thanks for pointing me to that.
Also you don't get an out-of-memory but a "java.lang.NegativeArraySizeException". That's interesting, I'll have to do
some more investigation why/how this is happening. I'll keep you posted.
Regards,
Dominik
On 23 Mar 2017, at 15:50, Sascha Neinert <sascha.neinert at uni-koeln.de<mailto:sascha.neinert at uni-koeln.de>> wrote:
Hi all,
we have imported an .scn file (approx. 11 GB) with the insight client (5.2.7) into our OMERO server (also 5.2.7). It is from a leica slidescanner. Importing, viewing and zooming works fine. A strange effect is that sometimes the export icon gets disabled and stays that way (the one with the red arrow down labeled „save the image as…"). I don’t know if it is related to some zooming in/out or just random.
Exporting as png has worked two times, zooming to max and then exporting lead to a crash (stacktrace is below). Should this work, or is exporting that format not (yet?) supported? Exporting to jpeg also did not work.
The script „batch image export“ just says „can’t export a ‚big‘ image to jpeg“ so maybe this is not related to .scn files but to any big file?
Thanks! Best regards, Sascha.
- - -
Exception when trying to export:
java.lang.Exception: Abnormal termination due to an uncaught exception.
java.lang.NegativeArraySizeException
at java.awt.image.DataBufferInt.<init>(DataBufferInt.java:75)
at java.awt.image.Raster.createPackedRaster(Raster.java:467)
at java.awt.image.DirectColorModel.createCompatibleWritableRaster(DirectColorModel.java:1032)
at java.awt.image.BufferedImage.<init>(BufferedImage.java:324)
at org.openmicroscopy.shoola.agents.imviewer.browser.BrowserModel.getDisplayedImage(BrowserModel.java:508)
at org.openmicroscopy.shoola.agents.imviewer.browser.BrowserComponent.getDisplayedImage(BrowserComponent.java:156)
at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerModel.getDisplayedImage(ImViewerModel.java:1417)
at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerComponent.getDisplayedImage(ImViewerComponent.java:1531)
at org.openmicroscopy.shoola.agents.imviewer.util.saver.ImgSaver.createImages(ImgSaver.java:253)
at org.openmicroscopy.shoola.agents.imviewer.util.saver.ImgSaver.saveImage(ImgSaver.java:474)
at org.openmicroscopy.shoola.agents.imviewer.util.saver.ImgSaverFileChooser.approveSelection(ImgSaverFileChooser.java:261)
at org.openmicroscopy.shoola.agents.imviewer.util.saver.ImgSaverUI.actionPerformed(ImgSaverUI.java:505)
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:6533)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
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:80)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:229)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:227)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:227)
at java.awt.Dialog.show(Dialog.java:1084)
at java.awt.Component.show(Component.java:1671)
at java.awt.Component.setVisible(Component.java:1623)
at java.awt.Window.setVisible(Window.java:1014)
at java.awt.Dialog.setVisible(Dialog.java:1005)
at org.openmicroscopy.shoola.util.ui.UIUtilities.setLocationRelativeTo(UIUtilities.java:634)
at org.openmicroscopy.shoola.util.ui.UIUtilities.setLocationRelativeToAndShow(UIUtilities.java:610)
at org.openmicroscopy.shoola.agents.imviewer.actions.SaveAction.actionPerformed(SaveAction.java:116)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$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:6533)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
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:80)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
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)
Abnormal termination due to an uncaught exception.
java.lang.NegativeArraySizeException
at java.awt.image.DataBufferInt.<init>(DataBufferInt.java:75)
at java.awt.image.Raster.createPackedRaster(Raster.java:467)
at java.awt.image.DirectColorModel.createCompatibleWritableRaster(DirectColorModel.java:1032)
at java.awt.image.BufferedImage.<init>(BufferedImage.java:324)
at org.openmicroscopy.shoola.agents.imviewer.browser.BrowserModel.getDisplayedImage(BrowserModel.java:508)
at org.openmicroscopy.shoola.agents.imviewer.browser.BrowserComponent.getDisplayedImage(BrowserComponent.java:156)
at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerModel.getDisplayedImage(ImViewerModel.java:1417)
at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerComponent.getDisplayedImage(ImViewerComponent.java:1531)
at org.openmicroscopy.shoola.agents.imviewer.util.saver.ImgSaver.createImages(ImgSaver.java:253)
at org.openmicroscopy.shoola.agents.imviewer.util.saver.ImgSaver.saveImage(ImgSaver.java:474)
at org.openmicroscopy.shoola.agents.imviewer.util.saver.ImgSaverFileChooser.approveSelection(ImgSaverFileChooser.java:261)
at org.openmicroscopy.shoola.agents.imviewer.util.saver.ImgSaverUI.actionPerformed(ImgSaverUI.java:505)
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:6533)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
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:80)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:229)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:227)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:227)
at java.awt.Dialog.show(Dialog.java:1084)
at java.awt.Component.show(Component.java:1671)
at java.awt.Component.setVisible(Component.java:1623)
at java.awt.Window.setVisible(Window.java:1014)
at java.awt.Dialog.setVisible(Dialog.java:1005)
at org.openmicroscopy.shoola.util.ui.UIUtilities.setLocationRelativeTo(UIUtilities.java:634)
at org.openmicroscopy.shoola.util.ui.UIUtilities.setLocationRelativeToAndShow(UIUtilities.java:610)
at org.openmicroscopy.shoola.agents.imviewer.actions.SaveAction.actionPerformed(SaveAction.java:116)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$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:6533)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
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:80)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
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)
Exception in thread "AWT-EventQueue-0"
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:189)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:289)
at org.openmicroscopy.shoola.env.AbnormalExitHandler.doTermination(AbnormalExitHandler.java:147)
at org.openmicroscopy.shoola.env.AbnormalExitHandler.terminate(AbnormalExitHandler.java:85)
at org.openmicroscopy.shoola.env.RootThreadGroup.uncaughtException(RootThreadGroup.java:69)
at java.awt.EventDispatchThread.processException(EventDispatchThread.java:223)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:215)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109)
at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:229)
at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:227)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:227)
at java.awt.Dialog.show(Dialog.java:1084)
at java.awt.Component.show(Component.java:1671)
at java.awt.Component.setVisible(Component.java:1623)
at java.awt.Window.setVisible(Window.java:1014)
at java.awt.Dialog.setVisible(Dialog.java:1005)
at org.openmicroscopy.shoola.util.ui.UIUtilities.setLocationRelativeTo(UIUtilities.java:634)
at org.openmicroscopy.shoola.util.ui.UIUtilities.setLocationRelativeToAndShow(UIUtilities.java:610)
at org.openmicroscopy.shoola.agents.imviewer.actions.SaveAction.actionPerformed(SaveAction.java:116)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$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:6533)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
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:80)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
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)
--
Sascha Neinert
CECAD RRZK IT Service
Regional Computing Center (RRZK)
University of Cologne
Phone: +49-221 478-84051 / +49-221 470-89624
Mail: sascha.neinert at uni-koeln.de<mailto:sascha.neinert at uni-koeln.de>
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