<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Martin,
<div class=""><br class="">
</div>
<div class=""> When you say you removed and installed omero-figure AND the web app,</div>
<div class="">I’m assuming you mean this (with a couple of other config settings):</div>
<div class=""><br class="">
</div>
<div class=""><span style="color: rgb(34, 34, 34); font-family: Monaco, 'Bitstream Vera Sans Mono', 'Lucida Console', Terminal, monospace; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class="">pip install omero-figure</span></div>
<div class=""><span style="color: rgb(34, 34, 34); font-family: Monaco, 'Bitstream Vera Sans Mono', 'Lucida Console', Terminal, monospace; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class="">bin/omero config append omero.web.apps
'"omero_figure"'</span></div>
<div class=""><br class="">
</div>
<div class="">Just wanted to be sure you’re not also downloading the app and adding it to PYTHONPATH</div>
<div class="">as you had to do for previous releases.</div>
<div class=""><br class="">
</div>
<div class="">When you’re looking for channel sliders and buttons in the Preview panel,</div>
<div class="">these will only show if you have 1 image selected OR if all the selected</div>
<div class="">images have the same number of channels.</div>
<div class=""><br class="">
</div>
<div class="">Does that explain the problem?</div>
<div class=""><br class="">
</div>
<div class="">If not, I wonder if you could open your browser’s dev tools (in Firefox or Chrome you can right-click anywhere on</div>
<div class="">the page and choose the “Inspect Element” option to open dev tools).</div>
<div class="">Then look in the Console and Network tabs when you refresh the page and select images</div>
<div class="">and see if there’s any errors there when you’re seeing the problem.</div>
<div class=""><br class="">
</div>
<div class="">Could you send us a screenshot of what you’re seeing.</div>
<div class=""><br class="">
</div>
<div class=""> Hope that helps,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 31 Jul 2017, at 15:18, Martin Wlotzka <<a href="mailto:martin.wlotzka@uni-heidelberg.de" class="">martin.wlotzka@uni-heidelberg.de</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Dear Kenny,<br class="">
<br class="">
I tried a complete requirements check and OMERO.figure reinstall<br class="">
(removed the web app, removed omero-figure via pip, server reboot,<br class="">
installed omero-figure and web app again), but that didn't change<br class="">
anything. The channel sliders and buttons are still missing.<br class="">
<br class="">
I uploaded the pip freeze output, the omero config output, the<br class="">
master.err and the Blitz log to OMERO QA. Hope you can find something...<br class="">
<br class="">
Best regards,<br class="">
<br class="">
Martin<br class="">
<br class="">
<br class="">
On 24.07.2017 15:30, Martin Wlotzka wrote:<br class="">
<blockquote type="cite" class="">Hi Kenny,<br class="">
<br class="">
yes there are indeed pyramid issues with Leica .lif images. However, I<br class="">
uploaded the good/bad pyramid files for the other mailing list post on<br class="">
"Pyramids, fast/slow rendering and image size".<br class="">
<br class="">
Regarding the OMERO.figure issue, I uploaded the nginx logs and the<br class="">
OMERO.web log:<br class="">
<br class="">
nginx_access.log<br class="">
nginx_error.log<br class="">
OMEROweb_inspect_figure_missing_buttons.log<br class="">
<br class="">
Thanks for the hint on the OMERO.web requirements, I'll check that.<br class="">
<br class="">
Best regards,<br class="">
Martin<br class="">
<br class="">
On 24.07.2017 12:14, Kenneth Gillen (Staff) wrote:<br class="">
<blockquote type="cite" class="">Hi Martin,<br class="">
<br class="">
<blockquote type="cite" class="">Leica_16bit_bad_pyramid.lif<br class="">
</blockquote>
Is this a file you’d expect OMERO to import, and properly render? The<br class="">
filename, `bad_pyramid` suggests you know of issues. I.e. is this<br class="">
something you`d like to the Bio-Formats team to look at? (a separate<br class="">
issue to the OMERO.figure issue perhaps?)<br class="">
<br class="">
For me, this image loads in an OMERO 5.3.3 with Figure 3.1.1 server,<br class="">
though (perhaps suggested by the filename), looks odd: yellowish<br class="">
background, random spots. However, I can add labels, rotate, zoom and edit<br class="">
the channels, which implies your Figure issue is not related to the image,<br class="">
but to the setup of Figure.<br class="">
<br class="">
<blockquote type="cite" class="">Leica_8bit_good_pyramid.lif<br class="">
</blockquote>
And this second image, when loading into the same server, I see error:<br class="">
`Image Leica_8bit_good_pyramid.lif is too big for OMERO.figure`. Is it<br class="">
happily loaded by your own OMERO.figure?<br class="">
<br class="">
<br class="">
The next thing I can think of is that some OMERO.web requirements are not<br class="">
satisfied.<br class="">
<br class="">
If you could confirm which versions of the OMERO.web requirements<br class="">
OMERO.web is configured to use, we can rule that out:<br class="">
<br class="">
e.g. your equivalent of: ~omero/omerowebvenv/bin/pip freeze<br class="">
<br class="">
Which will determine if you need to re-install/upgrade the OMERO.web<br class="">
requirements, outlined in the install docs ubuntu walkthrough [1].<br class="">
<br class="">
If re-installing the web requirements doesn’t yield and instant result, if<br class="">
you could also send us your OMERO configuration via omero config get<br class="">
--hide-password, and your server’s Blitz-0.log, and master.err<br class="">
<br class="">
<br class="">
[1]<br class="">
<a href="https://docs.openmicroscopy.org/omero/5.3.3/sysadmins/unix/install-web/walk" class="">https://docs.openmicroscopy.org/omero/5.3.3/sysadmins/unix/install-web/walk</a><br class="">
through/omeroweb-install-ubuntu-ice3.6.html or<br class="">
<br class="">
All the best,<br class="">
<br class="">
Kenny<br class="">
<br class="">
--<br class="">
<br class="">
Kenneth Gillen<br class="">
<br class="">
<br class="">
OME System Administrator<br class="">
<br class="">
Wellcome Trust Centre for Gene Regulation & Expression<br class="">
School of Life Sciences<br class="">
CTIR 2<br class="">
University of Dundee<br class="">
Dow Street<br class="">
Dundee DD1 5EH<br class="">
United Kingdom<br class="">
<br class="">
Tel: +44 (0) 1382 388797<br class="">
<br class="">
<br class="">
http://www.twitter.com/openmicroscopy<br class="">
<br class="">
----<br class="">
<br class="">
Dear Kenny,<br class="">
<br class="">
I've uploaded the logs:<br class="">
<br class="">
nginx_access.log<br class="">
nginx_error.log<br class="">
<br class="">
OMEROweb_inspect_figure_missing_buttons.log<br class="">
<br class="">
I also tried reinstalling, but that didn't change anything.<br class="">
<br class="">
Best,<br class="">
<br class="">
Martin<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 19/07/2017 17:08, "ome-users on behalf of Kenneth Gillen (Staff)"<br class="">
<ome-users-bounces@lists.openmicroscopy.org.uk on behalf of<br class="">
k.h.gillen@dundee.ac.uk> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">It would be worth retrying the install of the plugin at the least.<br class="">
<br class="">
Then I¹d be thinking about at least sending us a .tar.gz or .zip of your<br class="">
OMEROweb.log and your NGINX log. Perhaps there¹s something in the NGINX<br class="">
log, for example, which is showing 404s or 5xx responses which might point<br class="">
to what is going on.<br class="">
<br class="">
You can send us logs via http://qa.openmicroscopy.org.uk/qa/upload/<br class="">
<br class="">
It¹d be interesting to hear if anyone else has come across this one. My<br class="">
own OMERO server upgraded to this version without issues on RHEL7, rather<br class="">
than Ubuntu.<br class="">
<br class="">
<br class="">
All the best,<br class="">
<br class="">
Kenny<br class="">
<br class="">
--<br class="">
<br class="">
Kenneth Gillen<br class="">
<br class="">
OME System Administrator<br class="">
<br class="">
Wellcome Trust Centre for Gene Regulation & Expression<br class="">
School of Life Sciences<br class="">
CTIR 2<br class="">
University of Dundee<br class="">
Dow Street<br class="">
Dundee DD1 5EH<br class="">
United Kingdom<br class="">
<br class="">
Tel: +44 (0) 1382 388797<br class="">
<br class="">
<br class="">
http://www.twitter.com/openmicroscopy<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 19/07/2017 15:08, "ome-users on behalf of Martin Wlotzka"<br class="">
<ome-users-bounces@lists.openmicroscopy.org.uk on behalf of<br class="">
martin.wlotzka@uni-heidelberg.de> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Hi Kenny,<br class="">
<br class="">
yes I recently upgraded from 3.1.0 to 3.1.1, and the buttons / sliders<br class="">
were there in 3.1.0. I already tried downgrading again, but that didn't<br class="">
bring them back.<br class="">
<br class="">
-- Martin<br class="">
<br class="">
<br class="">
On 19.07.2017 15:55, Kenneth Gillen (Staff) wrote:<br class="">
<blockquote type="cite" class="">Hi Martin,<br class="">
<br class="">
Has OMERO.figure always been like this on this server? Was it, for<br class="">
example, installed, or upgraded recently?<br class="">
<br class="">
Many thanks<br class="">
<br class="">
Kenny<br class="">
<br class="">
--<br class="">
<br class="">
Kenneth Gillen<br class="">
<br class="">
<br class="">
OME System Administrator<br class="">
<br class="">
Wellcome Trust Centre for Gene Regulation & Expression<br class="">
School of Life Sciences<br class="">
CTIR 2<br class="">
University of Dundee<br class="">
Dow Street<br class="">
Dundee DD1 5EH<br class="">
United Kingdom<br class="">
<br class="">
Tel: +44 (0) 1382 388797<br class="">
<br class="">
<br class="">
http://www.twitter.com/openmicroscopy<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 19/07/2017 14:28, "ome-users on behalf of Martin Wlotzka"<br class="">
<ome-users-bounces@lists.openmicroscopy.org.uk on behalf of<br class="">
martin.wlotzka@uni-heidelberg.de> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">Dear all,<br class="">
<br class="">
when I open images in OMERO.figure, the sliders and buttons for<br class="">
channel<br class="">
adjustment, image rotation etc. are missing in the "Preview" window.<br class="">
There is only the zoom slider, no matter how many images I add to the<br class="">
page, and how many of them I select for editing. Any idea what could<br class="">
be<br class="">
the reason?<br class="">
<br class="">
I run OMERO 5.3.3 and Figure 3.1.1. on Ubuntu 16.04.<br class="">
<br class="">
Best regards,<br class="">
<br class="">
Martin<br class="">
<br class="">
_______________________________________________<br class="">
ome-users mailing list<br class="">
ome-users@lists.openmicroscopy.org.uk<br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</blockquote>
The University of Dundee is a registered Scottish Charity, No: SC015096<br class="">
_______________________________________________<br class="">
ome-users mailing list<br class="">
ome-users@lists.openmicroscopy.org.uk<br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</blockquote>
_______________________________________________<br class="">
ome-users mailing list<br class="">
ome-users@lists.openmicroscopy.org.uk<br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</blockquote>
The University of Dundee is a registered Scottish Charity, No: SC015096<br class="">
_______________________________________________<br class="">
ome-users mailing list<br class="">
ome-users@lists.openmicroscopy.org.uk<br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</blockquote>
The University of Dundee is a registered Scottish Charity, No: SC015096<br class="">
_______________________________________________<br class="">
ome-users mailing list<br class="">
ome-users@lists.openmicroscopy.org.uk<br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</blockquote>
_______________________________________________<br class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</blockquote>
<br class="">
_______________________________________________<br class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>