[ome-devel] image display problem
Curtis Rueden
ctrueden at wisc.edu
Mon Sep 11 21:00:56 BST 2006
Hi Bernd,
I was playing with Shoola today too and managed to get that same exception
by waiting about an hour after launching the program. My guess is that my
session timed out, and Shoola failed to retrieve things properly after that.
So I figure the exception is probably a fairly generic failure (I'm betting
the exception happens any time something goes wrong in the rendering
pipeline when communicating with the server). (Shoola developers: please
correct me if I am wrong.)
It seems clear there is something pretty funky about your installation on
the server side. If even the web client isn't working, it's probably not
worth your time to try the Java clients. You mentioned some LDAP errors -- I
thought OME didn't support LDAP without Mike McCaughey's patch. Are you
using that patch? If so, have you tested without it? Also, those LDAP errors
(to my untrained eye) didn't look particularly fatal.
Unfortunately, I can't really help much more with your install woes, since
the installer, web interface and Shoola all work on my Ubuntu system. Maybe
someone else can comment. Or maybe you can hack into the perl a little to
learn more information.
-Curtis
On 9/11/06, Bernd Jagla <baj2107 at columbia.edu> wrote:
>
> I have now tried shoola and get the following error message:
>
>
>
> Rendering Engine Exception: Can't load image metadata. Image id: 98
>
> org.openmicroscopy.shoola.env.rnd.metadata.MetadataSourceException: Can't
> retrieve the pixels metadata.
>
> at org.openmicroscopy.shoola.env.rnd.metadata.MetadataSource.load(
> MetadataSource.java:210)
>
> at org.openmicroscopy.shoola.env.rnd.metadata.MetadataSource.makeNew
> (MetadataSource.java:80)
>
> at org.openmicroscopy.shoola.env.rnd.Renderer.makeNew(Renderer.java
> :114)
>
> at org.openmicroscopy.shoola.env.rnd.RenderingManager.makeNew(
> RenderingManager.java:91)
>
> at org.openmicroscopy.shoola.env.rnd.RenderingEngine.handleLoadImage
> (RenderingEngine.java:137)
>
> at org.openmicroscopy.shoola.env.rnd.RenderingEngine.eventFired(
> RenderingEngine.java:242)
>
> at org.openmicroscopy.shoola.env.event.EventBusImpl.dispatch(
> EventBusImpl.java:185)
>
> at org.openmicroscopy.shoola.env.event.EventBusImpl.post(
> EventBusImpl.java:165)
>
> at org.openmicroscopy.shoola.agents.datamng.DataManager.viewImage(
> DataManager.java:1019)
>
> at
> org.openmicroscopy.shoola.agents.datamng.DataManagerCtrl.viewImage(
> DataManagerCtrl.java:333)
>
> at
> org.openmicroscopy.shoola.agents.datamng.TreePopupMenuManager.view(
> TreePopupMenuManager.java:173)
>
> at
> org.openmicroscopy.shoola.agents.datamng.TreePopupMenuManager.actionPerformed
> (TreePopupMenuManager.java:147)
>
> at javax.swing.AbstractButton.fireActionPerformed(
> AbstractButton.java:1849)
>
> at javax.swing.AbstractButton$Handler.actionPerformed(
> AbstractButton.java:2169)
>
> at javax.swing.DefaultButtonModel.fireActionPerformed(
> DefaultButtonModel.java:420)
>
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java
> :258)
>
> at javax.swing.AbstractButton.doClick(AbstractButton.java:302)
>
> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(
> BasicMenuItemUI.java:1000)
>
> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(
> BasicMenuItemUI.java:1041)
>
> at java.awt.Component.processMouseEvent(Component.java:5488)
>
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>
> at java.awt.Component.processEvent(Component.java:5253)
>
> at java.awt.Container.processEvent(Container.java:1966)
>
> at java.awt.Component.dispatchEventImpl(Component.java:3955)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2024)
>
> at java.awt.Component.dispatchEvent(Component.java:3803)
>
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java
> :4212)
>
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java
> :3892)
>
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
>
> at java.awt.Container.dispatchEventImpl(Container.java:2010)
>
> at java.awt.Window.dispatchEventImpl(Window.java:1774)
>
> at java.awt.Component.dispatchEvent(Component.java:3803)
>
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>
> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(
> EventDispatchThread.java:242)
>
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(
> EventDispatchThread.java:163)
>
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java
> :157)
>
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java
> :149)
>
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
> Caused by: org.openmicroscopy.is.ImageServerException:
> org.apache.commons.httpclient.HttpRecoverableException: Error in parsing
> the status line from the response: unable to find line starting with "HTTP"
>
> at org.openmicroscopy.is.HttpImageServer.executeCall(
> HttpImageServer.java:157)
>
> at org.openmicroscopy.is.HttpImageServer.getPixelsInfo(
> HttpImageServer.java:360)
>
> at org.openmicroscopy.is.HttpImageServer.getStackStatistics(
> HttpImageServer.java:1168)
>
> at org.openmicroscopy.is.PixelsFactory.getStackStatistics(
> PixelsFactory.java:803)
>
> at
> org.openmicroscopy.shoola.env.data.PixelsServiceAdapter.getStackStatistics
> (PixelsServiceAdapter.java:208)
>
> at org.openmicroscopy.shoola.env.rnd.metadata.MetadataSource.load(
> MetadataSource.java:198)
>
> ... 37 more
>
> Exception in thread "AWT-EventQueue-0"
>
>
>
>
>
> When importing the metamorph images I get following output after import
> (see the "unknown format", is this correct???), and still cant see the
> thumbnails:
>
>
>
> [bernd at BERND-HOME TestImages]$ ome import 011B1_Morph_*.TIF
>
> Importing files
>
> 1/15: [IN PROGRESS] Starting import
>
> 14/15: [IN PROGRESS] Importing
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
> line 378.
>
> 15/15: [IN PROGRESS] Executing import chain
>
> 15/15: [FINISHED] Imported 16 images from 12 files. 12 scanned. 12
> unknown format, 0 duplicates, 0 errors.
>
> Successfully Imported:
>
> 1345: 011B1_Morph_A01_s2
>
> 1346: 011B1_Morph_P01_s2
>
> 1347: 011B1_Morph_A01_s1
>
> 1348: 011B1_Morph_P01_s1
>
> 1349: 011B1_Morph_P01_s1_w2
>
> 1350: 011B1_Morph_A01_s1_w2
>
> 1351: 011B1_Morph_P01_s1_w3
>
> 1352: 011B1_Morph_P01_s1_w1
>
> 1353: 011B1_Morph_A01_s2_w2
>
> 1354: 011B1_Morph_A01_s1_w1
>
> 1355: 011B1_Morph_A01_s2_w3
>
> 1356: 011B1_Morph_P01_s2_w2
>
> 1357: 011B1_Morph_A01_s1_w3
>
> 1358: 011B1_Morph_A01_s2_w1
>
> 1359: 011B1_Morph_P01_s2_w3
>
> 1360: 011B1_Morph_P01_s2_w1
>
> Exiting...
>
> Exiting...
>
>
>
>
>
>
>
> Any ideas???
>
>
>
> Thanks,
>
>
>
> Bernd
>
>
>
> |-----Original Message-----
>
> |From: ome-devel-bounces at lists.openmicroscopy.org.uk [mailto:ome-devel-
>
> |bounces at lists.openmicroscopy.org.uk] On Behalf Of Bernd Jagla
>
> |Sent: Friday, September 08, 2006 10:44 AM
>
> |To: 'Curtis Rueden'
>
> |Cc: ome-devel at lists.openmicroscopy.org.uk
>
> |Subject: Re: [ome-devel] image display problem
>
> |
>
> |Curtis,
>
> |
>
> |I can see the image even though I have to adjust the intensities...
>
> |
>
> |I see this LDAP message in the error_log of httpd:
>
> |Can anyone make sense of this?
>
> |
>
> |Here is the error log from the following steps:
>
> |Remove /OME (rm -rf)
>
> |Dropdb ome
>
> |Sudo perl install -y
>
> |ome import ~/allOMEs/inca/Screening.ome
>
> |(=> no problems)
>
> |ome import ~/test/Ai_compound_import.ome
>
> |=> problems with
>
> |OME::Tasks::LSIDManager::getRemoteObject() is not implemented. at
>
> |/usr/lib/perl5/site_perl/5.8.6/OME/ImportExport/ModuleImport.pm line 183
>
> |
>
> |Could it be that this error comes up when doing the second import within
> a
>
> |certain timeframe? There is no error log entry when this error occurs.
>
> |
>
> |Thanks,
>
> |Bernd
>
> |
>
> |Ok here is finally the snippet from the error_log:
>
> |
>
> |
>
> |[Fri Sep 08 09:31:21 2006] [notice] Digest: generating secret for digest
>
> |authentication ...
>
> |[Fri Sep 08 09:31:21 2006] [notice] Digest: done
>
> |[Fri Sep 08 09:31:21 2006] [notice] LDAP: Built with OpenLDAP LDAP SDK
>
> |[Fri Sep 08 09:31:21 2006] [notice] LDAP: SSL support unavailable
>
> |[Fri Sep 08 09:31:22 2006] [notice] mod_python: Creating 4 session
> mutexes
>
> |based on 150 max processes and 0 max threads.
>
> |[Fri Sep 08 09:31:22 2006] [notice] Apache/2.0.54 (Fedora) configured --
>
> |resuming normal operations
>
> |Use of uninitialized value in print at
>
> |/home/bernd/allOMEs/06_08_18/OME/src/perl2/mod_perl_test.pl line 6.
>
> |Use of uninitialized value in print at
>
> |/home/bernd/allOMEs/06_08_18/OME/src/perl2/mod_perl_test.pl line 6.
>
> |[Fri Sep 08 09:31:22 2006] [error] [client 127.0.0.1] In PID 10585, Error
>
> |calling OMEIS: Method parameter missing
>
> |[Fri Sep 08 09:31:26 2006] [error] [client 127.0.0.1] In PID 10601, Error
>
> |calling OMEIS: Method parameter missing
>
> |[Fri Sep 08 09:31:44 2006] [notice] SIGHUP received. Attempting to
> restart
>
> |[Fri Sep 08 09:31:44 2006] [warn] The ScriptAlias directive in
>
> |/OME/conf/httpd2.omeis-dev.conf at line 2 will probably never match
> because
>
> |it overlaps an
>
> | earlier ScriptAlias.
>
> |Use of uninitialized value in concatenation (.) or string at
>
>
> |/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/ApacheConfigTask.pm
>
> |line 75.
>
> |Processing OME-startup.pl
>
> |DBD::Pg::st execute failed: ERROR: permission denied for relation
>
> |experimenters
>
> |Tring to get a session as the Apache user...
>
> |Pre-loading SemanticTypes...
>
> |WARNING: Explicit deletion of OME::Session at /OME/conf/OME-startup.plline
>
> |76
>
> |OME::Session __destroySession: $self->__destroySession();
>
> | at /OME/conf/OME-startup.pl line 76
>
> |Pre-loading classes for OME::Web...
>
> |[Fri Sep 08 09:31:47 2006] [notice] Digest: generating secret for digest
>
> |authentication ...
>
> |[Fri Sep 08 09:31:47 2006] [notice] Digest: done
>
> |[Fri Sep 08 09:31:47 2006] [notice] LDAP: Built with OpenLDAP LDAP SDK
>
> |[Fri Sep 08 09:31:47 2006] [notice] LDAP: SSL support unavailable
>
> |[Fri Sep 08 09:31:48 2006] [notice] mod_python: Creating 4 session
> mutexes
>
> |based on 150 max processes and 0 max threads.
>
> |[Fri Sep 08 09:31:48 2006] [notice] Apache/2.0.54 (Fedora) configured --
>
> |resuming normal operations
>
> |
>
> ||-----Original Message-----
>
> ||From: ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] On Behalf
>
> |Of
>
> ||Curtis Rueden
>
> ||Sent: Friday, September 08, 2006 9:40 AM
>
> ||To: Bernd Jagla
>
> ||Cc: ome-devel at lists.openmicroscopy.org.uk
>
> ||Subject: Re: [ome-devel] image display problem
>
> ||
>
> ||Hi Bernd,
>
> ||You could try reading the binary .ome files with VisBio from disk, to
> see
>
> ||how things look.
>
> ||-Curtis
>
> ||
>
> ||
>
> ||On 9/7/06, Bernd Jagla < baj2107 at columbia.edu
>
> |<mailto:baj2107 at columbia.edu>
>
> ||> wrote:
>
> ||
>
> || Hi there,
>
> ||
>
> ||
>
> ||
>
> || I managed to get the images from the INCell imported again with the
>
> ||new version of OME. The images are in OMEIS (verified). They 16 bit
> Tiffs.
>
> ||
>
> || The problem I have is that the images are not displayed on the
>
> |screen.
>
> ||They cannot be exported to VisBio. I get an XML from the download with
>
> |some
>
> ||binary data but can't confirm that this is what I want since I don't
> know
>
> ||how to read them. I believe that the attached error log has something to
>
> |do
>
> ||with this. I couldn't see anything interesting in the http error logs.
>
> ||
>
> ||
>
> ||
>
> || Please advise where look for possible solutions.
>
> ||
>
> ||
>
> ||
>
> || Thanks,
>
> ||
>
> ||
>
> ||
>
> || Bernd
>
> ||
>
> ||
>
> || _______________________________________________
>
> || ome-devel mailing list
>
> || ome-devel at lists.openmicroscopy.org.uk
>
> || http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
> ||
>
> ||
>
> ||
>
> ||
>
> ||
>
> |
>
> |
>
> |_______________________________________________
>
> |ome-devel mailing list
>
> |ome-devel at lists.openmicroscopy.org.uk
>
> |http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
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