[ome-devel] image display problem

Mon Sep 11 19:34:40 BST 2006

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(MetadataSourc
e.java:210)

      at
org.openmicroscopy.shoola.env.rnd.metadata.MetadataSource.makeNew(MetadataSo
urce.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(RenderingE
ngine.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.j
ava:1019)

      at
org.openmicroscopy.shoola.agents.datamng.DataManagerCtrl.viewImage(DataManag
erCtrl.java:333)

      at
org.openmicroscopy.shoola.agents.datamng.TreePopupMenuManager.view(TreePopup
MenuManager.java:173)

      at
org.openmicroscopy.shoola.agents.datamng.TreePopupMenuManager.actionPerforme
d(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:4
20)

      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.ja
va: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.jav
a:1168)

      at
org.openmicroscopy.is.PixelsFactory.getStackStatistics(PixelsFactory.java:80
3)

      at
org.openmicroscopy.shoola.env.data.PixelsServiceAdapter.getStackStatistics(P
ixelsServiceAdapter.java:208)

      at
org.openmicroscopy.shoola.env.rnd.metadata.MetadataSource.load(MetadataSourc
e.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.p
m 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...

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.pl line

|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

||

||

||

||

||

|

|

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