[ome-devel] image display problem

Ilya Goldberg igg at nih.gov
Tue Sep 12 17:33:52 BST 2006 

Hi Guys
All of the errors in the log that you sent are in fact normal. More  
comments inline.

You also said:
"The problem I have is that the images are not displayed on the screen"
Do you get the thumbnails?  What do they look like - an icon with a  
question mark inside?  A black square?  What happens if you click the  
lower-right corner of the square/icon/thumbnail - does it launch the  
SVG image viewer?
Click on the upper-left corner of the square/icon/thumbnail, and you  
should get the image detail view.
In the lower-right corner of this page (you may need to scroll down)  
it says "View with template:" followed by a drop-down menu, which  
says "detail".  Select "large" and click the Go button.  Still  
nothing?  Black square, or icon with question mark?

If instead of images, you get an icon with a question mark, then  
something may be wrong with the image server (OMEIS).
If you get a black square, it means that the default rendering  
settings were no good for your images.  You can fix this yourself  
temporarily by launching the SVG viewer, adjusting the color mapping  
and clicking "Save settings".
You can adjust these settings specifically in the InCell importer,  
which is probably a better idea.

Launching VisBio from the image view should work, but I'm not the  
best source if this is a problem.  It uses Java Web-Start to do its  
magic.
Shoola does not detect that its session expired, and gives a non- 
informative error.  You really have to not do anything with your  
logged in session from any client for over a half hour for the  
session to expire.  Every request refreshes the session, so it  
shouldn't expire in normal use.

Give a little more info about images not displaying, and we should be  
able to resolve that.
The InCell importer should have set the display options.  You can  
check this from the image detail view (select "detail" from the "View  
with template" menu when looking at an image).  On the upper-right  
click on "Image import" in the "Module Executions" table.  The  
Outputs table should have DisplayChannel and DisplayOptions listed in  
the "Untyped Outputs" column.  Click on DisplayOptions.  These two  
outputs specify how planes in your image are mapped to RGB channels  
for display.  Each plane in your image that's used for display is  
listed in "DisplayChannel" with its white level and black level.  The  
DisplayOptions table sets how each DisplayChannel is mapped to RGB.   
These two STs control how the image is displayed by the web UI and  
any other client that reads these settings.

Try importing one or more of the test images here:
http://openmicrosocpy.org/TestImages/
(maybe try the whole 011B1_Morph* set, which is a partial screening  
set from MetaMorph).  Are these displayed properly?

-Ilya



On Sep 8, 2006, at 10:43 AM, Bernd Jagla wrote:

> 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

This is a warning (not an error), and is normal and expected.


>
> 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

This is probably from mod_auth_ldap (not a part of OME).  Anyway,  
this doesn't look like an error.

> [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.

These appear sporadically and are generally harmless.  We try to get  
rid of them as we see them, but these apparently we missed.

> [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

These are the expected responses from OMEIS if the test is  
successful.  So when installing, this is a good thing.

> [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.

This one always comes up, and we haven't figured out what to do about  
it.  Anyway, its harmless because the installer copied the omeis  
binary to whatever ScriptAlias was set to (otherwise the above  
expected "Missing parameter" error would not have been generated by  
OMEIS).

> Use of uninitialized value in concatenation (.) or string at
> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/ 
> ApacheConfigTask.pm
> line 75.

Again, one of the ones we missed.  Harmless.

> Processing OME-startup.pl
> DBD::Pg::st execute failed: ERROR:  permission denied for relation
> experimenters

During the server startup, it tries to get an OME session as the user  
who launched apache.  Usually this is root, and usually this fails,  
so it tries to get a session as the Apache user:

> Tring to get a session as the Apache user...

And it succeeds as the Apache user, so all is well because it goes on  
to pre-load the STs:

> 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

This is also normal because we explicitly shut down the temporary DB  
handle we allocated to pre-load the STs.


> Pre-loading classes for OME::Web...

This is the last thing the pre-load script does, so all is well.

> [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

These are probably from mod_auth_ldap - has nothing to do with OME.

> [Fri Sep 08 09:31:48 2006] [notice] mod_python: Creating 4 session  
> mutexes
> based on 150 max processes and 0 max threads.

These are probably from mod_python - also has nothing to do with OME.


> [Fri Sep 08 09:31:48 2006] [notice] Apache/2.0.54 (Fedora)  
> configured --
> resuming normal operations

And this means we're good to go.


>
> |-----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
> |	http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> |
> |
> |
> |
> |
>
>
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