Images triggering very slow viewing in insight

[jacques2020]

Hi,

I experience a very slow retrieval of images in the images viewer ( about 40x slower than usual) and equally using the getPlane within matlab, with omero version 5.2.1. This is specific to some images since in the same session of insight, other images are accessed normally. The is nothing in the log of insight and I noted nothing in the Blitz.log although I am unsure to get everything. I attach the 10 important seconds. I clicked in Image viewer to change plane at 11:20:54 (time of the server), logged as user ID=2 (jacques), group ID=3 (CeDRE) and retrieving an image of user ID=153 (sylvain). Image ID was 195125. Of course there was some other activity by other user on the server at the same time. The issue is reproducible for this image specifically (and some others but always the same). I don't really know how to investigate this weird issue. I would be very happy to receive some advices.
Thank you very much

Best

Jacques

[Dominik]

Hi,

would it be possible to upload one of these images? ( https://www.openmicroscopy.org/qa2/qa/upload/ ) Are these all images of the same file type?

Regards,
Dominik

[jacques2020]

Dear Dominik,
thank you for your answer. The problem is a bit more complicated. If I can (slowly) see the images within omero, I cannot download the file. It I try, I get the error below in insight. Indeed, I considered the possibility of downloading the orignal file and re-importing but it seems not straightforward so far.
I don't know where to retrieve the image manually within the omero storage. If you can tell me that, I can either try re-importing and/or send you the image.

Best

Jacques

-------------------insight log ----------------------
java.lang.Exception: java.lang.Exception: java.lang.NullPointerException
at org.openmicroscopy.shoola.env.data.views.calls.ArchivedImageLoader$1.doCall(ArchivedImageLoader.java:170)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at java.util.ArrayList.addAll(ArrayList.java:577)
at org.openmicroscopy.shoola.env.data.views.calls.ArchivedImageLoader$1.doCall(ArchivedImageLoader.java:144)
... 7 more

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.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:257)
at org.openmicroscopy.shoola.env.ui.ActivityComponent.showException(ActivityComponent.java:403)
at org.openmicroscopy.shoola.env.ui.ActivityComponent.actionPerformed(ActivityComponent.java:924)
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:6535)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6300)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4891)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
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:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
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:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
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:76)
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)

[Dominik]

Interesting, I wonder if this is caused by the same underlying problem; I'll have a look at this problem, too. Anyway, you can find out the path of the original file with the "File path" button in the metadata panel (see attached screen shot). Would be great to get this image file for debugging purposes.

[jacques2020]

When I select the image and click on the "/.../." button (thanks for letting me notice this new to me and promising one!), I get the message "No information available." Is there an other way to explore the storage (to say the truth, I took a glimpse and it seems that original file name is not kept).

[Dominik]

So it's a file which was imported < OMERO 5 (I could have noticed by the the error log actually). Could you check the OMERO data directory on the server? It might be in a directory called .../Files/<image id> .

Regards,
Dominik

[jacques2020]

Hi Dominik,

I searched for the Image id and found e.g. 195126 in Files/Dir-195/ but not directly into Files/. I uploaed the corresponding file. About the omero version, it is a bit surprising that you think it is omero 5 since it is labelled in metadata as imported on 2011-07-06, which suggests an earlier version. I am also surprised by the size, 524 KB, while insight says uint16, 512x512, 4086 timepoints. These later quantities correspond to what I would expect for the experiments. Does that mean that the original file is lost and I only have the "display copy" omero 4 used to do ? Or is there a copy of the original file somewhere else ? I am somewhat disappointed.
Thank you for your help.

Jacques

PS: image uploaded were 195125, 195126 (both spanned image files from Andor iXon software during the same acquisition) and 195122 corresponding to an other acquisition.

[Dominik]

Hi,

yes, I meant, they must have been imported prior to OMERO 5. Thanks for uploading the files. However I think you are right, these are not the original files. I referred this topic to my colleagues, hopefully they can tell you, how you can access the files. Without the files or similar ones, which show the same slow loading problem, it will be difficult to debug. Thanks for your effort!

Regards,
Dominik

[Dominik]

Hi again,

do you have OMERO.web running, too? Because in OMERO.web you should be able to download the image, if it was imported with "archive" option (there's a bug in Insight, that's why you got this exception in first place). If the download option in web is greyed out however, the file was not imported with "archive" option originally. In that case I'm not sure if you can get the original image file at all.

Regards,
Dominik

[jacques2020]

Hi Dominik,

I can use omero web. The original problem of slow viewing is the same within omero web. I could download the original file and uploaded to you. It is named "20110624-gpa-16-1322.tif" and corresponds to the image 195125. Since this is not the only affected image, we should have the original file in all case (We always opted for archiving in omero the original file).

Thank you for your help!

Best

Jacques