[ome-users] OMERO.figure >> buttons and sliders in Preview window missing

[Martin Wlotzka]

Hi Kenny,

yes there are indeed pyramid issues with Leica .lif images. However, I
uploaded the good/bad pyramid files for the other mailing list post on
"Pyramids, fast/slow rendering and image size".

Regarding the OMERO.figure issue, I uploaded the nginx logs and the
OMERO.web log:

nginx_access.log
nginx_error.log
OMEROweb_inspect_figure_missing_buttons.log

Thanks for the hint on the OMERO.web requirements, I'll check that.

Best regards,
Martin

On 24.07.2017 12:14, Kenneth Gillen (Staff) wrote:
> Hi Martin,
>
>> Leica_16bit_bad_pyramid.lif
> Is this a file you’d expect OMERO to import, and properly render? The
> filename, `bad_pyramid` suggests you know of issues. I.e. is this
> something you`d like to the Bio-Formats team to look at?  (a separate
> issue to the OMERO.figure issue perhaps?)
>
> For me, this image loads in an OMERO 5.3.3 with Figure 3.1.1 server,
> though (perhaps suggested by the filename), looks odd: yellowish
> background, random spots. However, I can add labels, rotate, zoom and edit
> the channels, which implies your Figure issue is not related to the image,
> but to the setup of Figure.
>
>> Leica_8bit_good_pyramid.lif
> And this second image, when loading into the same server, I see error:
> `Image Leica_8bit_good_pyramid.lif is too big for OMERO.figure`. Is it
> happily loaded by your own OMERO.figure?
>
>
> The next thing I can think of is that some OMERO.web requirements are not
> satisfied.
>
> If you could confirm which versions of the OMERO.web requirements
> OMERO.web is configured to use, we can rule that out:
>
> e.g. your equivalent of: ~omero/omerowebvenv/bin/pip freeze
>
> Which will determine if you need to re-install/upgrade the OMERO.web
> requirements, outlined in the install docs ubuntu walkthrough [1].
>
> If re-installing the web requirements doesn’t yield and instant result, if
> you could also send us your OMERO configuration via omero config get
> --hide-password, and your server’s Blitz-0.log, and master.err
>
>
> [1]
> https://docs.openmicroscopy.org/omero/5.3.3/sysadmins/unix/install-web/walk
> through/omeroweb-install-ubuntu-ice3.6.html or
>
> All the best,
>
> Kenny
>
> --
>
> Kenneth Gillen
>
>
> OME System Administrator
>
> Wellcome Trust Centre for Gene Regulation & Expression
> School of Life Sciences
> CTIR 2
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> Tel: +44 (0) 1382 388797
>
>
> http://www.twitter.com/openmicroscopy
>
> ----
>
> Dear Kenny,
>
> I've uploaded the logs:
>
> nginx_access.log
> nginx_error.log
>
> OMEROweb_inspect_figure_missing_buttons.log
>
> I also tried reinstalling, but that didn't change anything.
>
> Best,
>
> Martin
>
>
>
>
>
>
>
> On 19/07/2017 17:08, "ome-users on behalf of Kenneth Gillen (Staff)"
> <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
> k.h.gillen at dundee.ac.uk> wrote:
>
>> It would be worth retrying the install of the plugin at the least.
>>
>> Then I¹d be thinking about at least sending us a .tar.gz or .zip of your
>> OMEROweb.log and your NGINX log. Perhaps there¹s something in the NGINX
>> log, for example, which is showing 404s or 5xx responses which might point
>> to what is going on.
>>
>> You can send us logs via http://qa.openmicroscopy.org.uk/qa/upload/
>>
>> It¹d be interesting to hear if anyone else has come across this one. My
>> own OMERO server upgraded to this version without issues on RHEL7, rather
>> than Ubuntu.
>>
>>
>> All the best,
>>
>> Kenny
>>
>> --
>>
>> Kenneth Gillen
>>
>> OME System Administrator
>>
>> Wellcome Trust Centre for Gene Regulation & Expression
>> School of Life Sciences
>> CTIR 2
>> University of Dundee
>> Dow Street
>> Dundee  DD1 5EH
>> United Kingdom
>>
>> Tel: +44 (0) 1382 388797
>>
>>
>> http://www.twitter.com/openmicroscopy
>>
>>
>>
>>
>>
>>
>>
>>
>> On 19/07/2017 15:08, "ome-users on behalf of Martin Wlotzka"
>> <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
>> martin.wlotzka at uni-heidelberg.de> wrote:
>>
>>> Hi Kenny,
>>>
>>> yes I recently upgraded from 3.1.0 to 3.1.1, and the buttons / sliders
>>> were there in 3.1.0. I already tried downgrading again, but that didn't
>>> bring them back.
>>>
>>> -- Martin
>>>
>>>
>>> On 19.07.2017 15:55, Kenneth Gillen (Staff) wrote:
>>>> Hi Martin,
>>>>
>>>> Has OMERO.figure always been like this on this server? Was it, for
>>>> example, installed, or upgraded recently?
>>>>
>>>> Many thanks
>>>>
>>>> Kenny
>>>>
>>>> --
>>>>
>>>> Kenneth Gillen
>>>>
>>>>
>>>> OME System Administrator
>>>>
>>>> Wellcome Trust Centre for Gene Regulation & Expression
>>>> School of Life Sciences
>>>> CTIR 2
>>>> University of Dundee
>>>> Dow Street
>>>> Dundee  DD1 5EH
>>>> United Kingdom
>>>>
>>>> Tel: +44 (0) 1382 388797
>>>>
>>>>
>>>> http://www.twitter.com/openmicroscopy
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 19/07/2017 14:28, "ome-users on behalf of Martin Wlotzka"
>>>> <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
>>>> martin.wlotzka at uni-heidelberg.de> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> when I open images in OMERO.figure, the sliders and buttons for
>>>>> channel
>>>>> adjustment, image rotation etc. are missing in the "Preview" window.
>>>>> There is only the zoom slider, no matter how many images I add to the
>>>>> page, and how many of them I select for editing. Any idea what could
>>>>> be
>>>>> the reason?
>>>>>
>>>>> I run OMERO 5.3.3 and Figure 3.1.1. on Ubuntu 16.04.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Martin
>>>>>
>>>>> _______________________________________________
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