[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
Mon Aug 23 14:12:44 BST 2010
Hi Ron,
The /OMERO/Pixels and /OMERO/Thumbnails will have corresponding
entries for each image imported,
but /OMERO/Files/ will not have corresponding entries.
This is the repository for additional files, used to annotate
Projects, Datasets, Images etc so it has nothing to do with your
problem.
I just tried to reproduce what you are seeing by deleting the /OMERO/
Pixels/ file for a particular image and then opening it in Insight.
It seems that you don't get any errors (only a blank image with all
the pixel values set to 0)!
This is a bug - You should have got some error - I've made a ticket.
http://trac.openmicroscopy.org.uk/shoola/ticket/1559
But this doesn't explain why OMERO is not able to find the 4.1 pixel
data.
One possibility is permissions on the pixel files.
Are there any differences in file permissions between the old 4.1
files in /OMERO/Pixels and the new ones you've imported with 4.2?
And are all the 4.2 pixel files being put in the same place as the 4.1
pixel files? (all in /OMRO/Pixels/ )?
Any other differences you can find between 4.1 and 4.2 pixel data?
Chris, Josh - Any possibility that some preferences or other
configuration could be pointing to an invalid location for the 4.1
pixel data?
Cheers,
Will.
On 23 Aug 2010, at 03:36, Taylor, Ronald C wrote:
>
> Will,
>
> As my PNNL colleague Steve Wiley told me late on Friday (I see that
> Steve Cced the omero list, so you should have seen his email), we
> can enter new images into 4.2.0 on the Mac server and see them OK.
> The image problem is confined to the images that got carried over
> from the 4.1.1 install. Those are the completely dark images.
>
> So - I'm thinking that the problem is not image display settings per
> se, but rather that 4.2.0 cannot find the old images to display. As
> I mentioned earlier, the previously entered images do get listed
> properly on-screen - but they show up as just black boxes. There are
> still entries for each old image in the db, but perhaps no path to
> the actual pixels?
>
> Question: I'm assuming that the actual pixel image gets stored in a
> flat file in the directory
> omero.data.dir/Pixels
>
> which would be this directory on our Mac server:
>
> /OMERO/Pixels
>
> I also noticed that there are many entries in ../Pixels (all the old
> images?) which lack a corresponding file in
> /OMERO/Files
>
> That is, there is, for example, a file
>
> /OMERO/Pixels/101 (and a file /OMERO/Thumbnails/101)
>
> But no file
>
> /OMERO/Files/101
>
> Should not each ../Pixels file have a corresponding entry in ../Files?
>
> Any thoughts on what to check in this regard?
>
> 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
>
>
> -----Original Message-----
> From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
> Sent: Saturday, August 21, 2010 3:31 AM
> To: Taylor, Ronald C
> Cc: 'Josh Moore'; ome-users at lists.openmicroscopy.org.uk; ronald.taylor24 at gmail.com
> ; Wiley, Steven
> Subject: Re: [ome-users] Query re the OMERO upgrade to OMERO 4.2.0
> on a Mac server - images are completely dark
>
> 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
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee DD1 5EH
United Kingdom
Phone 01382 386364
http://openmicroscopy.org.uk
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