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<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
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<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=""> In your dev tools console, could you paste in</div>
<div class=""><br class="">
</div>
<div class="">JST["src/templates/image_display_options_template.html”]</div>
<div class=""><br class="">
</div>
<div class="">and hit enter:</div>
<div class="">I get something like this returned:</div>
<div class=""><br class="">
</div>
<div class=""> function(obj) {..</div>
<div class=""><br class="">
</div>
<div class="">but I think you might not get this?</div>
<div class=""><br class="">
</div>
<div class="">Also, could you open the templates.js in your browser,</div>
<div class="">probably at</div>
<div class=""><a href="http://omero01.urz.uni-heidelberg.de/static/figure/templates.js" class="">http://omero01.urz.uni-heidelberg.de/static/figure/templates.js</a> </div>
<div class=""><br class="">
</div>
<div class="">and search for:</div>
<div class=""><br class="">
</div>
<div class="">src/templates/image_display_options_template.html</div>
<div class=""><br class="">
</div>
<div class="">you should find this line:</div>
<div class="">
<pre style="orphans: 2; widows: 2; word-wrap: break-word; white-space: pre-wrap;" class="">this["JST"]["src/templates/image_display_options_template.html"] = function(obj) {</pre>
<div class=""><br class="">
</div>
</div>
<div class="">Let me know if you do or not?</div>
<div class=""><br class="">
</div>
<div class="">I’m thinking the browser (or something else) has cached an old version of this templates.js.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">After uninstalling the figure app, the templates.js at the url above should not return (404).</div>
<div class="">When you install the figure app again, and do</div>
<div class=""><br class="">
</div>
<div class="">bin/omero web start</div>
<div class=""><br class="">
</div>
<div class="">or even</div>
<div class=""><br class="">
</div>
<div class="">bin/omero syncmedia</div>
<div class=""><br class="">
</div>
<div class="">this should copy over the new files from the omero_figure app into your static location,</div>
<div class="">so you should see this line included…</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">Copying '/usr/local/lib/python2.7/site-packages/omero_figure/static/figure/templates.js'</div>
<div class="">...</div>
</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>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 1 Aug 2017, at 12:58, 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="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p class="">Dear Will,</p>
<p class="">thanks for your advice! Please find my answers inlined.</p>
<p class="">Best, Martin<br class="">
</p>
<br class="">
<div class="moz-cite-prefix">On 01.08.2017 13:17, William Moore (Staff) wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk" 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>
</blockquote>
Yes.<br class="">
<blockquote type="cite" cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk" class="">
<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>
</blockquote>
No, there are no old PYTHONPATH / manually installed plugin relicts.<br class="">
<blockquote type="cite" cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk" class="">
<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>
</blockquote>
No, selecting any number of images (0,1, or more) doesn't change it. <br class="">
<blockquote type="cite" cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk" class="">
<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>
</blockquote>
In the dev tools console tab I see:<br class="">
<br class="">
Use of getPreventDefault() is deprecated. Use defaultPrevented instead. new<br class="">
Empty string passed to getElementById(). jquery-1.11.1.js:2798:12<br class="">
XML Parsing Error: not well-formed<br class="">
Location: <a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/figure/imgData/3315/?_=1501587400825">
http://omero01.urz.uni-heidelberg.de/figure/imgData/3315/?_=1501587400825</a><br class="">
Line Number 1, Column 1: 3315:1:1<br class="">
TypeError: this.template is not a function[Learn More] figure.js:6863:24<br class="">
render <a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:6863:24">
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:6863:24</a><br class="">
render <a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:5301:52">
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:5301:52</a><br class="">
triggerEvents <a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:203:32">
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:203:32</a><br class="">
trigger <a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:146:19">
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:146:19</a><br class="">
notifySelectionChange <a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:686:13">
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:686:13</a><br class="">
later <a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/underscore-1.3.3.js:561:25">
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/underscore-1.3.3.js:561:25</a><br class="">
<blockquote type="cite" cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk" class="">
<div class=""><br class="">
</div>
<div class="">Could you send us a screenshot of what you’re seeing.</div>
</blockquote>
Uploaded to my QA account (user mwlotzka) screenshots with the info, the preview and the labels tab:<br class="">
screenshot_OMERO_figure_info_seems_OK.png<br class="">
screenshot_OMERO_figure_preview_missing_buttons_and_sliders.png<br class="">
screenshot_OMERO_figure_labels_missing_everything.png
<blockquote type="cite" cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk" class="">
<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 class="">
<blockquote type="cite" class="">
<div class="">On 31 Jul 2017, at 15:18, Martin Wlotzka <<a href="mailto:martin.wlotzka@uni-heidelberg.de" class="" moz-do-not-send="true">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="" moz-do-not-send="true">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="">
<a class="moz-txt-link-freetext" href="http://www.twitter.com/openmicroscopy">http://www.twitter.com/openmicroscopy</a><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="">
<<a class="moz-txt-link-abbreviated" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> on behalf of<br class="">
<a class="moz-txt-link-abbreviated" href="mailto:k.h.gillen@dundee.ac.uk">k.h.gillen@dundee.ac.uk</a>> 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 <a class="moz-txt-link-freetext" href="http://qa.openmicroscopy.org.uk/qa/upload/">
http://qa.openmicroscopy.org.uk/qa/upload/</a><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="">
<a class="moz-txt-link-freetext" href="http://www.twitter.com/openmicroscopy">http://www.twitter.com/openmicroscopy</a><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="">
<<a class="moz-txt-link-abbreviated" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> on behalf of<br class="">
<a class="moz-txt-link-abbreviated" href="mailto:martin.wlotzka@uni-heidelberg.de">martin.wlotzka@uni-heidelberg.de</a>> 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="">
<a class="moz-txt-link-freetext" href="http://www.twitter.com/openmicroscopy">http://www.twitter.com/openmicroscopy</a><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="">
<<a class="moz-txt-link-abbreviated" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> on behalf of<br class="">
<a class="moz-txt-link-abbreviated" href="mailto:martin.wlotzka@uni-heidelberg.de">martin.wlotzka@uni-heidelberg.de</a>> 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="">
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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