EPU images

[aseedb]

What would be the procedure to import gain-corrected MRC stacks from EPU? The automatic import as well as import from EPU seem not to read parameters from the image headers. In the library table all numerical parameters are 0 or 1 (pixel size). Pixel size and number of frames are yet written in the header. I do not know if this is related but then when I try to drift correct with any of the 3 possible programs I am getting an error : ERROR: First provide gain-corrected stack as FASTDISK/raw_gaincorrectedstack.mrcs Note, the images were successfully imported as raw_gaincorrectedstack.mrcs (but in the project folder root, not on FASTDISK)

[sthennin]

hi, You are the first person, using EPU and contacting us. If you could send us a few example EPU data (MRC stack and metadata XML files?), then I could adjust the "Import from EPU" script for you. Please send to Henning.stahlberg@unibas.ch Thanks,

Henning.

[aseedb]

Hi Henning, OK thanks, I'm sending you this. Benoit

[rdrighetto]

Hi Benoit,

I just pushed an update to Github, the installation packages should be updated within ~1h or you can build from source. The "Import Movie from EPU" script now works, tested on the data you sent us. I'm just not 100% sure if the dose is being computed correctly, so could you please confirm that the results are as expected (check e.g. "total_dose") and close this ticket if so?

Best wishes,

-- Ricardo Diogo Righetto

2017-12-04 14:17 GMT+01:00 aseedb notifications@github.com:

Hi Henning, OK thanks, I'm sending you this. Benoit

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[aseedb]

Hi Ricardo,

Many thanks for your quick update! I tried and it worked. Well it crashed near the end of the procedure because of a python problem but I am sure the problem is on my side (wrong python version sourced) and I did not have time to fix it. I will close the issue when I am sure it goes seemless until the end.

Cheers

[aseedb]

Hi Ricardo, The procedure works fine now, I can confirm it. There is one minor problem: when importing the images, the xml files are moved to the import folder, even if the option to delete the original images is not selected. Wouldn't it make more sense to copy the xml files in this case? Best

[rdrighetto]

Hi Benoit,

Thanks for the feedback, glad to know the script works! I totally agree that this behavior of moving the .xml files around is not consistent with the "delete the original images" option in the Import GUI. However fixing that is not so straightforward as it may require changes in the Import backend code, and I'm out of the office at the moment so won't be able to work on this soon. In the meantime, to get the desired behavior you can double click the "Import Movie from EPU" script on the FOCUS GUI (when processing an individual image, e.g. after double-clicking it in the library), it should open the script in a text editor (otherwise, the path of the script is scripts/image/import/import_epu.script under your FOCUS installation directory). Then just change line 124 from

    \mv -f ${import_rawstack_original:r}.xml .

to

    \cp -f ${import_rawstack_original:r}.xml .

Please note that you may lose this change if you update FOCUS if you don't backup the modified script.

-- Ricardo Diogo Righetto

2017-12-06 23:29 GMT+01:00 aseedb notifications@github.com:

Hi Ricardo, The procedure works fine now, I can confirm it. There is one minor problem: when importing the images, the xml files are moved to the import folder, even if the option to delete the original images is not selected. Wouldn't it make more sense to copy the xml files in this case? Best

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[aseedb]

Hi Ricardo, Alright thank you!Cheers Benoît 

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Le jeudi, décembre 7, 2017, 9:15 AM, Ricardo Righetto notifications@github.com a écrit :

Hi Benoit,

Thanks for the feedback, glad to know the script works! I totally agree that this behavior of moving the .xml files around is not consistent with the "delete the original images" option in the Import GUI. However fixing that is not so straightforward as it may require changes in the Import backend code, and I'm out of the office at the moment so won't be able to work on this soon. In the meantime, to get the desired behavior you can double click the "Import Movie from EPU" script on the FOCUS GUI (when processing an individual image, e.g. after double-clicking it in the library), it should open the script in a text editor (otherwise, the path of the script is scripts/image/import/import_epu.script under your FOCUS installation directory). Then just change line 124 from

\mv -f ${import_rawstack_original:r}.xml .

to

\cp -f ${import_rawstack_original:r}.xml .

Please note that you may lose this change if you update FOCUS if you don't backup the modified script.

-- Ricardo Diogo Righetto

2017-12-06 23:29 GMT+01:00 aseedb notifications@github.com:

Hi Ricardo, The procedure works fine now, I can confirm it. There is one minor problem: when importing the images, the xml files are moved to the import folder, even if the option to delete the original images is not selected. Wouldn't it make more sense to copy the xml files in this case? Best

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/C-CINA/focus/issues/205#issuecomment-349796228, or mute the thread https://github.com/notifications/unsubscribe-auth/AHVvfwDpajWOSUro9Az1VQvZ5Zo91tRkks5s9xU3gaJpZM4Q0Y6x .

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