Feature #1413: make gain correction on dd raw frame mrc images into mrc stack - Appion - Electron Microscopy Group

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Feature #1413

closed

make gain correction on dd raw frame mrc images into mrc stack

Added by Anchi Cheng over 13 years ago. Updated over 10 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Amber Herold

Category:

Web interface

Target version:

Appion/Leginon 2.2.0

Start date:

10/04/2012

Due date:

% Done:

100%

Estimated time:

(Total: 0.00 h)

Description

Niko's request so that he can process the image stack of frames at will.

Subtasks 1 (0 open — 1 closed)

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Updated by Anchi Cheng almost 13 years ago

Category set to Web interface
Status changed from New to Assigned
Priority changed from Normal to Low
Target version set to Appion/Leginon Future Version

Need appionweb gui of the results or I will forget where the files are.

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Updated by Anchi Cheng over 12 years ago

test on project Cheng-12.03.19 (ap351) session 12may08e

makeDDRawFrameStack.py --preset=d2 --limit=1 --runname=ddstack1 --rundir=/ami/data00/appion/12may08e/ddstack/ddstack1 --expid=9911 --commit --projecid=351

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Updated by Anchi Cheng over 12 years ago

Assignee changed from Anchi Cheng to Amber Herold
Priority changed from Low to Urgent
Target version changed from Appion/Leginon Future Version to Appion/Leginon 2.2.0

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Updated by Amber Herold over 12 years ago

Checked in what I have so far. Still to do:

Add a query into the new database table to use when creating the runname.
Add the results of the "test single image" feature. need to check that the mrc file that ends in "_st.mrc" is in the rundir.
Add a report page like particleReport.php. Report the number of images processed by counting the number of files in the run directory.
Modify the side menu to include a link to the results report page.

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Updated by Anchi Cheng over 12 years ago

turns out I didn't finish what r16630 promised to do. r16660 added the rest of database commit part. You should find apDDStackRunData and apDDStackParamsData. preset should show in the report as well.

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Updated by Amber Herold over 12 years ago

Assignee changed from Amber Herold to Anchi Cheng

Anchi,
Trying to run from web or command line on Guppy myamisnap gives this result:

[amber@guppy ~]$ /opt/myamisnap/bin/appion makeDDRawFrameStack.py --description="test" --projectid=351 --preset=gr --session=12may08e --runname=ddstack2 --rundir=/ami/data00/appion/12may08e/ddstack/ddstack2 --no-rejects --no-wait --commit --limit=4 --continue --expid=9911 --jobtype=makeddrawframestack
Traceback (most recent call last):
  File "/opt/myamisnap/bin/makeDDRawFrameStack.py", line 9, in ?
    from appionlib import apDDprocess
  File "/opt/myamisnap/lib/appionlib/apDDprocess.py", line 18, in ?
    from leginon import correctorclient
  File "/opt/myamisnap/lib/leginon/correctorclient.py", line 14, in ?
    import instrument
  File "/opt/myamisnap/lib/leginon/instrument.py", line 16, in ?
    import gui.wx.Events
  File "/opt/myamisnap/lib/leginon/gui/wx/Events.py", line 14, in ?
    import wx
ImportError: No module named wx

Please assign back to me when updated with fix...

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Updated by Amber Herold over 12 years ago

r16675 Adds correct runname, a report page and a link to the report page from the side menu panel.

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Updated by Anchi Cheng over 12 years ago

Status changed from Assigned to In Code Review
Assignee changed from Anchi Cheng to Jim Pulokas

r16676 avoid loading instrument module in correctorclient.py globally. Only import it when needed. This work around is needed because processing clusters like guppy do not have wx installed.

Jim, please review this revision only and then assign back to Amber to finish Web interface.

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