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Is uploadRelionRefine.py implemented? #4849

Open leginonbot opened 8 months ago

leginonbot commented 8 months ago

Author Name: Philip Baldwin (@prbprb2) Original Redmine Issue: 4849, https://emg.nysbc.org/redmine/issues/4849 Original Date: 2017-03-22 Original Assignee: Neil Voss

Am trying to modify it to an uploadCryoSparc.py, but am not sure of the status. In any case, it is in the trunk.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2017-03-22T14:03:26Z

@myami/appion/bin/uploadRelionRefine.py@

works for me, but I doubt many people use it.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Philip Baldwin (@prbprb2) Original Date: 2017-03-22T15:08:37Z

Hi Neil, Thanks for answering. What button on the left side bar does it correspond to? Is there an uploadCRelionRefine.php that creates the command involving u?

Can you give me an example usage of uploadRelionRefine.py along with params? I don't happen to see a Relion section on the uploadrecon.php interface.

Thank you in advance, Phil

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2017-03-22T15:13:00Z

I have not used it in a while, so it would take awhile to figure out again, but it was designed to figure out most everything if you ran it from the Relion refinement folder. See #2044 for any documentation.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2017-03-22T15:13:44Z

Oh, I did not create a web launcher for it. We never figured that part out.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Philip Baldwin (@prbprb2) Original Date: 2017-03-22T15:23:04Z

The web launcher is the easy part isn't it? The uploadRelionRefine.py command is a lot longer than the launcher would be.

Thank you, Philip

Hi Neil,

Do you mind if I do a rewrite? Most of Amber's starFile.py should be supplanted by pandas dataframe shouldn't it? It is a standardized spreadsheet reader/writer.

Sincerely, Philip

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2017-04-01T20:57:11Z

I am not a big fan of the pandas software, frankly I have never used it. I thought it was for visualization of data rather than input/output. If you think it would be better or faster go ahead, but I was fine with how amber did the starFile.py