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I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.i2pc.es
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No thumbnails in html report #2052

Open tarhil opened 4 years ago

tarhil commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

tarhil commented 4 years ago

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 commented 4 years ago

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

tarhil commented 4 years ago

no errors, seems everything ok.

pconesa commented 4 years ago

Do you see any log lines like:

"Generating images for mic xxxxx" ?

tarhil commented 4 years ago

Do you see any log lines like:

"Generating images for mic xxxxx" ?

no

azazellochg commented 4 years ago

Could you please attach full run.stdout?

On Fri, Sep 20, 2019, 12:22 tarhil notifications@github.com wrote:

Do you see any log lines like:

"Generating images for mic xxxxx" ?

no

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tarhil commented 4 years ago

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 commented 4 years ago

Which protocols did you select in the summary monitor?

tarhil commented 4 years ago

I included results from import, motioncor, gctf.

pconesa commented 4 years ago

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 notifications@github.com escribió:

I included results from import, motioncor, gctf.

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azazellochg commented 4 years ago

@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 commented 4 years ago

@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 commented 4 years ago

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

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@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..

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tarhil commented 4 years ago

@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? :)

scipion

@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 commented 4 years ago

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

Are all 3 empty?

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

pconesa commented 4 years ago

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

tarhil commented 4 years ago

Thanks @tarhil , can you confirm that the /Runs/XXXXProtMonitorSummary/extra/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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

That works

pconesa commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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?