Full viewer in OMERO.Web after upgrade to 5.0.0

[dsudar]

Hi,
I just upgraded my 4.4.10 installation to version 5.0.0 and most of it went just fine. In Insight everything appears to work perfectly (still more testing to be done) but in OMERO.Web I have the problem that in the Full Viewer" no images appear at all. The thumbnails are all fine and in the Preview tab the image appears fine but in the Full Viewer I get a grey empty image after a brief "Loading ..." message.

My diagnostics says:

================================================================================
OMERO Diagnostics 5.0.0-ice34-b19
================================================================================

Commands: java -version 1.7.0 (/usr/bin/java)
Commands: python -V 2.7.3 (/usr/bin/python)
Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin)
Commands: psql --version 9.1.12 (/usr/bin/psql -- 2 others)

Server: icegridnode running
Server: Blitz-0 active (pid = 26589, enabled)
Server: DropBox active (pid = 26614, enabled)
Server: FileServer active (pid = 26613, enabled)
Server: Indexer-0 active (pid = 26621, enabled)
Server: MonitorServer active (pid = 26643, enabled)
Server: OMERO.Glacier2 active (pid = 26622, enabled)
Server: OMERO.IceStorm active (pid = 26625, enabled)
Server: PixelData-0 active (pid = 26623, enabled)
Server: Processor-0 active (pid = 26641, enabled)
Server: Tables-0 active (pid = 26627, enabled)
Server: TestDropBox inactive (enabled)

OMERO: SSL port 4064
OMERO: TCP port 4063

Log dir: /home/omero/OMERO.server/var/log exists

Log files: Blitz-0.log 9.0 MB errors=0 warnings=453
Log files: DropBox.log 1.0 KB
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 87.0 KB errors=0 warnings=2
Log files: MonitorServer.log 1.0 KB
Log files: OMEROweb.log 221.0 KB errors=6 warnings=22
Log files: OMEROweb_request.log 0.0 KB errors=0 warnings=1
Log files: PixelData-0.log 4.0 KB
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 10.00 MB


Environment:OMERO_HOME=/home/omero/OMERO.server
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/jdk1.7.0_11/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/home/omero/OMERO.server/bin
Environment:ICE_HOME=/usr/share/Ice-3.4.2
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/data/OMERO' Exists? True Is writable? True
OMERO temp dir: '/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
OMERO.web status... [RUNNING] (PID 2489)

and the errors in OMEROWeb.log include stuff such as:

2014-03-22 00:21:09,702 ERROR [ omero.gateway] (proc.27052) getThumbnail:6414 Traceback (most recent call last):
File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 6409, in getThumbnail
rv = thumb(*args)
File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 3541, in __call__
return self.handle_exception(e, *args, **kwargs)
File "/home/omero/OMERO.server/lib/python/omeroweb/webclient/webclient_gateway.py", line 1894, in handle_exception
e, *args, **kwargs)
File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 3538, in __call__
return self.f(*args, **kwargs)
File "/home/omero/OMERO.server/lib/python/omero_api_ThumbnailStore_ice.py", line 215, in getThumbnailByLongestSide
return _M_omero.api.ThumbnailStore._op_getThumbnailByLongestSide.invoke(self, ((size, ), _ctx))
InternalException: exception ::omero::InternalException
{
serverStackTrace = ome.conditions.InternalException: Wrapped Exception: (java.lang.RuntimeException):
ome.io.nio.DimensionsOutOfBoundsException: T '13' greater than sizeT '3'.
at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:248)

I'm suspecting something related to PIL and Pillow since I wasn't all the clear how to upgrade that.

Any suggestions I can try?
Thanks,
- Damir

[wmoore]

This seems very strange that the "Preview" tab viewer is working but the main viewer is not, since they use the same code.

Does the image viewer actually load a grey image - or is this failing to load any image at all? Can you right click on the image and "Open Image in New Tab"? Does this show a grey image?

Or you could try to see the rendered image directly by using the url:

<your-server>/webclient/render_image/<imageId>/0/0/

and see if this shows an image or an error on screen. Also you could check the logs when you refresh this page to be sure you're seeing appropriate errors in the logs.

It may also be useful to look for javascript errors by turning on the developer tools console in your browser.

Thanks,

Will.

[dsudar]

Hi Will,

Thanks for the quick reply and I'm embarrassed to admit that there apparently is no problem at all. I probably had a temporary glitch with the browser I was using or something like that. Today everything works fine. Pretty much as you suggest per your comment about looking at javascript errors in the browser. Apologies for the false alarm.

Just because I'm still a bit unclear about the PIL vs. Pillow issues: how can I see whether my python has the correct version of this add-on? When I went through the 4.4.10 to 5.0.0 upgrade I did the following on my Ubuntu 12.04 server:
apt-get remove python-imaging
pip install Pillow
Is that all?

Finally, I noticed a discrepancy in the documentation for the command-line importer on: http://www.openmicroscopy.org/site/supp ... mport.html
It refers to arguments "--plate_name" and "--plate_description" which are no longer accepted by the importer. Instead the arguments -n and -x now serve those roles. Just needs a small update of the docs.

Thanks again,
- Damir

[manics]

Hi Damir

Code: Select all

apt-get remove python-imaging
pip install Pillow


Should ensure you're using Pillow. One thing to be aware of with pip is that it compiles Pillow from source which means you may need to install some additional -dev packages, otherwise some functionality in OMERO will be missing. For instance the web image viewer may only partially work.

If you have problems could you try installing the following packages (the actual package names may vary though they should all be in the standard repositories):

• libpng-dev
• libjpeg-dev
• libtiff-dev
• zlib1g-dev

and then reinstall pillow:

Code: Select all

pip uninstall pillow
pip install pillow


I'll add a note to update our docs to cover installation of pillow, and also to fix the import discrepancy- thanks for pointing this out.

Note for anyone reading this in a few weeks after Ubuntu 14.04 LTS comes out: it looks like the python-imaging package has been changed to use Pillow so hopefully you won't need to worry about this.

Simon

[manics]

One more thing: If you want to be absolutely sure you're using Pillow the following line of code should print out the current version:

Code: Select all

python -c 'import PIL; print PIL.PILLOW_VERSION'