Open Microscopy Environment

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NB This was submitted with wrong title
it was incorrectly title as a problem with OMERO.figure
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Hi,

we've recently upgraded out server to 5.4.9 and are testing OMERO.iviewer. There are some images that don't open with OMERO.iviewer - it fails with the message
"Failed to get image data".

The images open in

image viewer (the original one)
OMERO.figure
FPBioimage

From a very cursory test, it seems to be limited to Nikon confocal images. I've uploaded an example here to the qa site, it's called 'tile006.nd2'. For some reason the qa site didn't give a reference link like it normally does (or I've forgotten how to do it).

Any suggests for a log file to look in?

Cheers,

Chris

evenhuis wrote:Hi,

Hi Chris.

we've recently upgraded out server to 5.4.9 and are testing OMERO.iviewer. There are some images that don't open with OMERO.iviewer - it fails with the message
"Failed to get image data".

What version of iviewer do you have installed?

I've uploaded an example here to the qa site, it's called 'tile006.nd2'. For some reason the qa site didn't give a reference link like it normally does (or I've forgotten how to do it).

We successfully received the image, thanks for sending that. Sorry that the confirmation wasn't obvious - it usually emails you a reference if you've given it your email address. Perhaps it's ended up in the s-p-a-m folder.

I imported this image into the OMERO demo server [1] @ OMERO 5.4.9 and OMERO.iviewer 0.5.0. It seemed to load okay in OMERO.iviewer, and I had a play around changing the channel colour to the `thermal` LUT as an example workflow. It seemed to work to me, though it took a few (6) seconds to load - we're working on a performance improvement on that particular system. You're welcome to replicate this test with the Demo server if you like - link below.

Any suggests for a log file to look in?

If you already have iviewer 0.5.0, the latest release, then the best we can do is the OMERO.web log on the server, and the browser's developer toolbar for javascript debugging. I'd be hoping for something in the developer toolbar to flag up any client-side javascript issues that don't hit the server log. More experience web developers than myself will be better taking this thread up if you've exhaused the above avenues.

All the best,

Kenny

[1] https://help.openmicroscopy.org/demo-server.html

Hi Kenny,

thanks for the tips. We are running OMERO.iviewer 0.5.0.

I won't be able to check the server logs until tomorrow.

There are some errors javascript errors in the browser. I checked this in Safari and Firefox and both give the same two errors.

Below is the console output from Firefox which is a bit more detailed and I could copy it more easily.

Thanks,

Chris

Code: Select all

{"delta_t_unit_symbol": null, "init_zoom": 0, "tiles": false, "families": ["polynomial", "logarithmic", "linear", "exponential"], "roi_count": 0, "perms": {"canAnnotate": true, "canEdit": true, "canDelete": true, "canLink": true}, "rdefs": {"defaultT": 0, "model": "color", "invertAxis": false, "projection": "normal", "defaultZ": 8}, "pixel_range": [0, 65535], "interpolate": true, "channels": [{"coefficient": 1.0, "active": true, "window": {"max": 4095.0, "end": 4095.0, "start": 20.0, "min": 20.0}, "family": "linear", "color": "0000FF", "inverted": false, "reverseIntensity": false, "emissionWave": 450.0, "label": "Hoechst33258"}, {"coefficient": 1.0, "active": true, "window": {"max": 90.0, "end": 90.0, "start": 26.0, "min": 26.0}, "family": "linear", "color": "FFFFFF", "inverted": false, "reverseIntensity": false, "emissionWave": null, "label": "TD"}], "meta": {"projectName": "Nikon_A1", "imageId": 93002, "imageAuthor": "XXXXXXX", "imageTimestamp": 1540173399.0, "pixelsType": "uint16", "datasetId": 2901, "projectDescription": "", "datasetName": "XXX", "wellSampleId": "", "projectId": 970, "imageDescription": "", "wellId": "", "imageName": "tile006.nd2", "datasetDescription": ""}, "id": 93002, "pixel_size": {"symbol_y": "\u00b5m", "symbol_x": "\u00b5m", "symbol_z": "\u00b5m", "unit_y": 0.****************, "unit_x": 0.****************, "unit_z": 10.0, "y": 0.****************, "x": 0.****************, "z": 10.0}, "size": {"width": 1024, "c": 2, "z": 17, "t": 1, "height": 1024}, "split_channel": {"c": {"width": 2054, "gridy": 2, "border": 2, "gridx": 2, "height": 2054}, "g": {"width": 2054, "gridy": 1, "border": 2, "gridx": 2, "height": 1028}}, "import_date": "2018-10-22 02:56:39", "delta_t": []} main.js:9:28199
error https://omero.research.uts.edu.au/static/omero_iviewer/main.js:9:28199
h https://omero.research.uts.edu.au/static/omero_iviewer/main.js:88:23333
fireWith https://omero.research.uts.edu.au/static/omero_iviewer/main.js:88:24087
n https://omero.research.uts.edu.au/static/omero_iviewer/main.js:88:59515
e/< https://omero.research.uts.edu.au/static/omero_iviewer/main.js:88:64362

TypeError: this.image_config is null[Learn More] main.js:185:75186
app/thumbnail-slider/</l</i.prototype.onImageConfigChange
https://omero.research.uts.edu.au/static/omero_iviewer/main.js:185:75186
app/thumbnail-slider/</l</i.prototype.bind/this.selected_image_observer<
https://omero.research.uts.edu.au/static/omero_iviewer/main.js:185:74690
m
https://omero.research.uts.edu.au/static/omero_iviewer/main.js:104:3718
7/dt</t.prototype.call
https://omero.research.uts.edu.au/static/omero_iviewer/main.js:104:49108
19/c</t.prototype._flushQueue
https://omero.research.uts.edu.au/static/omero_iviewer/main.js:9:18455
19/c</t.prototype.flushMicroTaskQueue
https://omero.research.uts.edu.au/static/omero_iviewer/main.js:9:19191
t/this.requestFlushMicroTaskQueue< https://omero.research.uts.edu.au/static/omero_iviewer/main.js:9:18104


Hi Chris,

Thanks for the javascript error - I suspect that's more informative than anything we'll find server-side. But not harm in checking the server side logs too once you've got access.

If there are any other actions required than a plain import to trigger the issue, let me know what I can do to try to replicate this. e.g. does re-importing the image you sent us, and loading it freshly into iviewer do the same thing?

Someone on the OME team will take a look at this as soon as they can - we have a slightly smaller team at the moment while we attend http://www.nibb.ac.jp/abis/gbi-abis_training?lang=en in Japan.

Best,

Kenny

Hi Kenny,

no worries.

I've tried a fresh import under my name just in case it was a permission but it still fails to load. We have a dev server as well which replicates the issue.

Maybe it's the bioformats version? I'll check if we a re update tomorrow.

Cheers,

Chris

Hi Chris,

evenhuis wrote:Maybe it's the bioformats version? I'll check if we a re update tomorrow.

It's interesting that it's format-dependent, certainly. Unless you're running a custom Bio-Formats version, our 5.4.9 server should be running the same version of Bio-Formats as your server, so it's odd that it works for ours, but not for yours.

There have been some recent changes to the code that appears to be generating the error, so if you have control over the version of iviewer that's running, you could install the previous version, or the version before that, and re-try. (Perhaps on your development server?)

We would try that if we could replicate the issue.

Best,

Kenny

Hi Kenny,

Version roll back
0.4.1 : problem persists.
0.3.0 : problem persists, other images not opening.

demo server
As you said, the image uploads can be viewed.

OMERO.web logs
here's what gets logged when the 'tile006.nd' is opened with iViewer

Code: Select all

2018-10-23 01:25:18,801  INFO [                           omero.gateway] (proc.129977) connect():2219 created connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:18,972  INFO [                           omero.gateway] (proc.129981) connect():2219 created connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:19,070  INFO [                           omero.gateway] (proc.129979) connect():2219 created connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:19,082  INFO [                           omero.gateway] (proc.129979) close():1932 closed connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:19,099  INFO [                           omero.gateway] (proc.129977) close():1932 closed connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:19,160  INFO [                           omero.gateway] (proc.129979) connect():2219 created connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:19,161  INFO [                           omero.gateway] (proc.129977) connect():2219 created connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:19,299  INFO [                           omero.gateway] (proc.129977) _register_service():1583 Registered 0d41139a-9dac-40a2-b2df-9966c4b7c6a7/dfb47eea-fb05-428c-9a1f-bcef16a13aeeomero.api.RenderingEngine -t -e 1.0:tcp -h 10.223.80.24 -p 45708 -t 60000
2018-10-23 01:25:19,338  INFO [                           omero.gateway] (proc.129981) close():1932 closed connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:19,444  INFO [                           omero.gateway] (proc.129979) close():1932 closed connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:19,461  INFO [                           omero.gateway] (proc.129977) _register_service():1583 Registered 0d41139a-9dac-40a2-b2df-9966c4b7c6a7/26e4fed3-7358-4968-900a-9b8f5af6de14omero.api.RawPixelsStore -t -e 1.0:tcp -h 10.223.80.24 -p 45708 -t 60000
2018-10-23 01:25:19,505  INFO [                           omero.gateway] (proc.129977) _unregister_service():1592 Unregistered 0d41139a-9dac-40a2-b2df-9966c4b7c6a7/26e4fed3-7358-4968-900a-9b8f5af6de14omero.api.RawPixelsStore -t -e 1.0:tcp -h 10.223.80.24 -p 45708 -t 60000
2018-10-23 01:25:19,647  INFO [                           omero.gateway] (proc.129977) _unregister_service():1592 Unregistered 0d41139a-9dac-40a2-b2df-9966c4b7c6a7/dfb47eea-fb05-428c-9a1f-bcef16a13aeeomero.api.RenderingEngine -t -e 1.0:tcp -h 10.223.80.24 -p 45708 -t 60000
2018-10-23 01:25:19,649  INFO [                           omero.gateway] (proc.129977) close():1932 closed connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:20,464  INFO [                           omero.gateway] (proc.129979) connect():2219 created connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:20,479  INFO [                           omero.gateway] (proc.129979) close():1932 closed connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:20,709  INFO [                           omero.gateway] (proc.129977) connect():2219 created connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)
2018-10-23 01:25:20,723  INFO [                           omero.gateway] (proc.129977) close():1932 closed connection (uuid=0d41139a-9dac-40a2-b2df-9966c4b7c6a7)


Cheers,

Chris

Hi Chris,

The only other thing that I can think of would be to check the OMERO.web prerequisites.

Getting the list of prerequisites from: https://docs.openmicroscopy.org/omero/5 ... yment.html

Here are ours - and you/we can compare with yours?

Code: Select all

#Logging in and changing directory to the location we installed OMERO.web
[kenny@ome-demoserver web]$ cd /opt/omero/web

#Activating the virtualenv our web install runs under:
[kenny@ome-demoserver web]$ source venv/bin/activate

(venv)[kenny@ome-demoserver web]$ pip freeze | grep -Ei "(pillow|ice|django|numpy|matplotlib)"
Django==1.8.18
Pillow==2.0.0
django-cors-headers==2.4.0
django-pipeline==1.3.20
django-prometheus==1.0.14
django-redis==4.8.0
matplotlib==1.2.0
numpy==1.7.1
zeroc-ice==3.6.3

Hi Kenny,

Heres the versions of the libraries we have installed:

Cheers,

Chris

Code: Select all

pip freeze | grep -Ei "(pillow|ice|django|numpy|matplotlib)"pip freeze | grep -Ei "(pillow|ice|django|numpy|matplotlib)"

Django==1.8.18
django-cors-headers==2.1.0
django-pipeline==1.3.27
django-redis==4.8.0
matplotlib==1.2.0
numpy==1.7.1
Pillow==2.0.0
zeroc-ice==3.6.4


Hi Chris,

Comparing that list against the requirements in the code:

There's a very specific version of django-pipeline as a requirement - not sure why, but I'd recommend removing django-pipeline and installing that particular version.

https://github.com/openmicroscopy/openm ... y27.txt#L9

Also, I clearly didn't capture all the requirements in my grep statement: there are more to check:

Code: Select all

(venv)-bash-4.2$  pip freeze | grep -Ei "(pillow|ice|django*|numpy|matplotlib|omero*|gunicorn)" | sort

Django==1.8.18
django-cors-headers==2.4.0
django-pipeline==1.3.20
django-prometheus==1.0.14
django-redis==4.8.0
gunicorn==19.7.1
matplotlib==1.2.0
numpy==1.7.1
omero-figure==4.0.0
omero-fpbioimage==0.3.0
omero-iviewer==0.5.0
omero-marshal==0.5.3
omero-parade==0.1.2
omero-webtagging-autotag==3.0.2
omero-webtagging-tagsearch==3.0.3
Pillow==2.0.0


I've applied a "sort" to make comparison easier between our output.

* I noticed while reviewing the requirements file for this post, our own numpy version is outdated. I'll need to work out how to add that into our upgrade process [1].

Best,

Kenny

[1] https://github.com/openmicroscopy/prod- ... issues/118