No thumbnails in html report #2052

tarhil · 2019-09-18T14:55:15Z

Hi,
I just installed the latest scipion version from git on a debian stretch system.
To evaluate microscope performance I started a standard workflow of import movies, motioncor2, gctf and monitor summary.
Everything runs like a charm, however I have no thumbnails in the index.html
All thumbnail folders are empty.

Any ideas?

azazellochg · 2019-09-18T14:59:18Z

Hi @tarhil, my guess would be you are missing eman2 which is now used to make thumbnails. If you install it and rerun monitor it should work

tarhil · 2019-09-18T15:18:18Z

Hi @tarhil, my guess would be you are missing eman2 which is now used to make thumbnails. If you install it and rerun monitor it should work

Thanks for the reply, sadly eman2.3 was installed via the plugin manager.

pconesa · 2019-09-18T16:30:15Z

Hi! @tarhil Scipion should be able to use eman2.3 for the thumbnails

tarhil · 2019-09-18T18:54:11Z

Hi! @tarhil Scipion should be able to use eman2.3 for the thumbnails

Oh, that was misleading. Just wanted to make clear that eman is installed and the problem must be something else...

pconesa · 2019-09-19T06:29:52Z

I see....Do you see any hint in the logs of the monitor summary?

tarhil · 2019-09-19T06:58:46Z

no errors, seems everything ok.

pconesa · 2019-09-20T09:21:55Z

Do you see any log lines like:

"Generating images for mic xxxxx" ?

tarhil · 2019-09-20T09:22:37Z

Do you see any log lines like:

"Generating images for mic xxxxx" ?

no

azazellochg · 2019-09-20T09:28:57Z

Could you please attach full run.stdout?

…

On Fri, Sep 20, 2019, 12:22 tarhil ***@***.***> wrote: Do you see any log lines like: "Generating images for mic xxxxx" ? no — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2052?email_source=notifications&email_token=ABVBPJUAZTWE7ENHNSTAL63QKSI55A5CNFSM4IX77URKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7GD5XI#issuecomment-533479133>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABVBPJWSSTWNYCSQJ33Z57LQKSI55ANCNFSM4IX77URA> .

tarhil · 2019-09-26T11:39:35Z

ESC[32mRUNNING PROTOCOL -----------------ESC[0m
HostName: sambia
PID: 17644
Scipion: v2.0 (2019-04-23) Diocletian
currentDir: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS
workingDir: Runs/000190_ProtMonitorSummary
runMode: Restart
MPI: 1
threads: 1
Starting at step: 1
Running steps
ESC[35mSTARTEDESC[0m: monitorStep, step 1
2019-09-25 09:37:32.239072
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
ESC[32mRUNNING PROTOCOL -----------------ESC[0m
HostName: sambia
PID: 20732
Scipion: v2.0 (2019-04-23) Diocletian
currentDir: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS
workingDir: Runs/000190_ProtMonitorSummary
runMode: Continue
MPI: 1
threads: 1
len(steps) 1 len(prevSteps) 1
Starting at step: 1
Running steps
ESC[35mSTARTEDESC[0m: monitorStep, step 1
2019-09-25 09:40:47.504419
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
Writing report html to: /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/index.html
(END)

pconesa · 2019-09-26T14:15:39Z

Which protocols did you select in the summary monitor?

tarhil · 2019-09-26T18:51:17Z

I included results from import, motioncor, gctf.

pconesa · 2019-09-27T01:36:07Z

Thank you tarhil. I fail to see what can be wrong there. Is there any chance we can ssh your machine to check more technical stuff? El jue., 26 sept. 2019 20:51, tarhil <[email protected]> escribió:

…

I included results from import, motioncor, gctf. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2052?email_source=notifications&email_token=AAF7ZYNMPB6XOLPQ6534HHLQLUACNA5CNFSM4IX77URKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7WTBHY#issuecomment-535638175>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAF7ZYMTYV6XI5TWUBJWBJTQLUACNANCNFSM4IX77URA> .

azazellochg · 2019-09-27T16:53:03Z

@tarhil above is run.log, could you paste run.stdout which is more detailed?
Also, by no thumbnails you mean Micrographs table has no images or the whole report page has no images/plots? Maybe a screenshot? :)

azazellochg · 2019-09-27T17:02:04Z

@pconesa if I use a default browser (Konqueror) on a remote host then I have no plots/images at all - I guess JS is not enabled/working there. But in Firefox/Chrome all is ok. However, I think @tarhil has a different issue here..

delarosatrevin · 2019-09-27T17:12:29Z

Could be that some thumbnails are linked and not copied under rsync (default options)?

…

On Fri, Sep 27, 2019 at 7:02 PM Gregory Sharov ***@***.***> wrote: @pconesa <https://github.com/pconesa> if I use a default browser (Konqueror) on a remote host then I have no plots/images at all - I guess JS is not enabled/working there. However I think @tarhil <https://github.com/tarhil> has a different issue here.. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2052?email_source=notifications&email_token=ACAM6WDXSMOOHVV4B5N6BPTQLY4A3A5CNFSM4IX77URKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ZQLDI#issuecomment-536020365>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACAM6WDP2H3YII6OUKJXSZDQLY4A3ANCNFSM4IX77URA> .

tarhil · 2019-09-28T18:37:59Z

@tarhil above is run.log, could you paste run.stdout which is more detailed?
Also, by no thumbnails you mean Micrographs table has no images or the whole report page has no images/plots? Maybe a screenshot? :)

@delarosatrevin
thumbnails are calculated by the original jobs (motioncor, gctf) but not copied into the monitor subfolders. Currently I am trying things on a local machine, therefore no rsync needed.

pconesa · 2019-09-29T04:47:41Z

Thanks @tarhil , can you confirm that the /Runs/XXXXProtMonitorSummary/extra/<PROJECT_NAME>imgXXXThumbs

Are all 3 empty?

If not the issue is around the html....otherwise we should focus on the generation of it.

pconesa · 2019-09-29T04:49:19Z

May be this will work:
ls /data/test/Krios/2019-09-24_AFIS/Krios_AFIS/Runs/000190_ProtMonitorSummary/extra/Krios_AFIS/img*

tarhil · 2019-09-29T08:06:37Z

Thanks @tarhil , can you confirm that the /Runs/XXXXProtMonitorSummary/extra/<PROJECT_NAME>imgXXXThumbs

Are all 3 empty?

If not the issue is around the html....otherwise we should focus on the generation of it.

All are empty, I checked this already.

pconesa · 2019-09-29T16:50:50Z

Thanks again, @tarhil .....let's try to test the thumbnail generation. In a terminal type (adapt the path, please):

scipion python -c "from pyworkflow.em.convert import ImageHandler; ih = ImageHandler(); ih.computeThumbnail('/extra/data/tests/relion13_tutorial/betagal/Micrographs/Falcon_2012_06_12-16_59_12_0.mrc','/tmp/thumb2.png')"

pconesa · 2019-09-29T16:53:40Z

This should generate a thumbnail in a similar way as the summary protocol does. It should be at /tmp/thumb2.png

Please, replace /extra/data/tests/relion13_tutorial/betagal/Micrographs/Falcon_2012_06_12-16_59_12_0.mrc with a valid path to a micrograph. If you can use one of the mics used in the project that fails is will be better.

tarhil · 2019-10-17T17:57:07Z

That works

pconesa · 2019-10-18T07:21:07Z

thanks @tarhg I must admit this bug is hard to catch.

Is there any chance we can access your machine to debug in-situ your case? (ssh, teamviewer, VNC)

tarhil · 2019-11-12T20:36:33Z

sorry for the late response. At the moment unfortunately not, no remote access due to new firewall policies... I am still trying to get it.

pconesa · 2020-01-09T08:46:05Z

I guess this is not fixed yet, right. @tarhil
Are you able to edit some code files? to try to understand why this is failing?

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No thumbnails in html report #2052

No thumbnails in html report #2052

tarhil commented Sep 18, 2019

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No thumbnails in html report #2052

No thumbnails in html report #2052

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