[ome-users] Query re the OMERO upgrade to OMERO 4.2.0 on a Mac server - images are completely dark
Will Moore
will at lifesci.dundee.ac.uk
Sat Aug 21 11:30:40 BST 2010
Hi Ron,
I'm not sure what's going on - I would expect to see some error,
but you're not seeing anything like that?
Are you actually getting the pixel data (with messed-up rendering
settings) or is all the pixel data zeros?
Try to use adjust the rendering settings, or use the measurement tool
to see if you actually have pixel values there
E.g. http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-0/mov/
MeasurementTool-Taking%20Measurments.mov
Will.
On 20 Aug 2010, at 22:34, Taylor, Ronald C wrote:
>
> Forgot to include diagnostics output - so, resending my help
> request with diags output at bottom.
> Ron
>
> -----Original Message-----
> From: Taylor, Ronald C
> Sent: Friday, August 20, 2010 2:22 PM
> To: 'Josh Moore'; ome-users at lists.openmicroscopy.org.uk
> Cc: ronald.taylor24 at gmail.com; Taylor, Ronald C; Wiley, Steven
> Subject: RE: [ome-users] need help with the OMERO upgrade to OMERO
> 4.2.0 on a Mac server - images are completely dark
>
>
> Hi Josh, everybody,
>
> Got 4.2.0 up and running on our Mac server, but initial testing
> shows that all our images come up completely dark. The images are
> still there - the file names get listed on-screen, but they appear
> on-screen as completely dark image boxes - no way to actually see
> them.
>
> So - this problem did not occur in the 4.2.0 upgrade on our Linux
> box. But the problem is definitely there on our Mac. Even when I do
> a "launch full viewer" the images come up black. Any ideas on what
> I should check?
>
> Does this perhaps have something to do with telling OMERO where its
> data directory is? I have checked the
> /Library/Omero/Versions/4.2.0/omero_dist/etc/omero_properties
>
> file, which shows
> omero.data.dir set to "/OMERO/"
>
> which appears to be correct - that was the previous setting for
> 4.1.1, and the subdirs in /OMERO/ show dates of "Aug20" (today), so
> Omero must have been accessing those directories today when I was
> testing the system. However, I see that all the thumbnail files
> have dates of today. Is that correct, or is something going wrong?
> The image files were previously in 4.1.1, so should not the
> thumbnails have been created long ago?
>
> Anyhoo - could use more guidance.
> Ron
>
> ___________________________________________
> Ronald Taylor, Ph.D.
> Computational Biology & Bioinformatics Group Pacific Northwest
> National Laboratory
> 902 Battelle Boulevard
> P.O. Box 999, Mail Stop J4-33
> Richland, WA 99352 USA
> Office: 509-372-6568
> Email: ronald.taylor at pnl.gov
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>
> bash-3.2$ omero admin diagnostics
>
> ======================================================================
> ==========
> OMERO Diagnostics Beta-4.2.0-r7571-b29
> ======================================================================
> ==========
>
> Commands: java -version 1.6.0 (/usr/bin/java
> -- 2 others)
> Commands: python -V 2.6.1 (/usr/bin/python)
> Commands: icegridnode --version 3.3.1 (/Library/Ice/
> Versions/3.3.1/bin/icegridnode)
> Commands: icegridadmin --version 3.3.1 (/Library/Ice/
> Versions/3.3.1/bin/icegridadmin)
> Commands: psql --version 8.3.11 (/Postgres/bin/
> psql)
>
> Server: icegridnode running
> Server: Blitz-0 active (pid = 21006,
> enabled)
> Server: DropBox active (pid = 21007,
> enabled)
> Server: FileServer active (pid = 21008,
> enabled)
> Server: Indexer-0 active (pid = 21009,
> enabled)
> Server: MonitorServer active (pid = 21010,
> enabled)
> Server: OMERO.Glacier2 active (pid = 21011,
> enabled)
> Server: OMERO.IceStorm active (pid = 21012,
> enabled)
> Server: Processor-0 active (pid = 21013,
> enabled)
> Server: Repository-1 error: node `repo'
> couldn't be reached:
> the node is not active
> Server: Tables-0 active (pid = 21014,
> enabled)
> Server: TestDropBox inactive (enabled)
>
> Log dir: /Library/Omero/Versions/4.2.0/omero_dist/var/log exists
>
> Log files: Blitz-0.log 1.0 MB
> errors=15 warnings=14
> Log files: DropBox.log 2.0 KB
> errors=1 warnings=3
> Log files: FileServer.log 0.0 KB
> Log files: Indexer-0.log 5.0 KB
> errors=0 warnings=9
> Log files: MonitorServer.log 2.0 KB
> errors=1 warnings=2
> Log files: OMEROweb.log 8.0 KB
> errors=22 warnings=0
> Log files: Processor-0.log 0.0 KB
> Log files: Tables-0.log 0.0 KB
> Log files: TestDropBox.log n/a
> Log files: master.err 0.0 KB
> Log files: master.out 0.0 KB
> Log files: Total size 1.22 MB
>
> Parsing Blitz-0.log:[line:17] => Server restarted <=
>
> Environment:OMERO_HOME=(unset)
>
> Environment:OMERO_NODE=(unset)
>
> Environment:OMERO_MASTER=(unset)
>
> Environment:PATH=/Library/Omero/Versions/4.2.0/omero_dist/bin:/usr/
> bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Postgres/bin:/
> Library/Java/Home/bin:/System/Library/Frameworks/JavaVM.framework/
> Versions/Current/Commands:/Library/Ice/Versions/3.3.1/bin
>
> Environment:ICE_HOME=/Library/Ice/Versions/3.3.1
>
> Environment:LD_LIBRARY_PATH=(unset)
>
> Environment:DYLD_LIBRARY_PATH=/Library/Frameworks/BerkeleyDB/
> Versions/4.6.21.NC/lib:/Library/Frameworks/expat/Versions/2.0.1/
> lib:/Library/PostgreSQL/Versions/8.3.11/lib:/Library/mcpp/Versions/
> 2.7.2/lib:/Library/Ice/Versions/3.3.1/lib:/Library/Frameworks/HDF5/
> Versions/1.8.4_patch1/lib
>
> bash-3.2$
> ----:**-F1 shell1 Bot
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