[ome-devel] image display problem

[Bernd Jagla]

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
|
|
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|	ome-devel at lists.openmicroscopy.org.uk
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|
|
|
|
|