[ome-devel] image display problem

Thu Sep 14 16:58:05 BST 2006

Ilya,

Thanks for the response. The thumbnails have a red X. Lower right click
gives a white image with the RGB values set correctly. I loaded the sample
files (see images below: *Morph*.TIF) from a completely new install (dropdb
ome, and rm -rf /OME)

I can try it again from a completely new directory structure to get rid of
the changes I made (I only added INCellRunXM.pm and changed
CoreDatabaseTablesTask.pm), but would like to hear from you first.

Is there a way to test OMEIS, since you mentioned that this might be the
problem?

Thanks again,

Bernd

|-----Original Message-----

|From: Ilya Goldberg [mailto:igg at nih.gov]

|Sent: Tuesday, September 12, 2006 12:34 PM

|To: Bernd Jagla

|Cc: 'Curtis Rueden'; ome-devel at lists.openmicroscopy.org.uk

|Subject: Re: [ome-devel] image display problem

|

|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

|> |

|> |

|> |  _______________________________________________

|> |  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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