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Task #1844 (closed)

Opened 14 years ago

Closed 14 years ago

CTF correction by EMAN2

Reported by: wmoore Owned by: wmoore
Priority: n.a. Milestone: Unscheduled
Component: n.a. Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
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Description (last modified by wmoore)

Use EMAN2 to do CTF correction on a bunch of images in OMERO.

This is the next step in the EMAN2 single particle workflow to support via OMERO.

Need to

  • get images in hand, with a list of file names
  • pass filenames as arguments to ctf command line
  • retrieve the result of running the ctf command ? and upload back to the server!

commands for basic ctf (lots more arguments supported)
http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2ctf

In UI workflow, ctf command line calls are done through
lib/emsprworkflow.py

WorkFlowTask.spawn_task(self,program,options,string_args,bool_args,additional_args=[],temp_file_name="e2workflow_tmp.txt"):

where the command arguments look something like

/Applications/EMAN2//EMAN2.cvs/bin/e2ctf.py bdb:particles#1160_ptcls --oversamp=1 --ac=10.0 --apix=2.0 --cs=1.0 --voltage=200.0 --autohp --autofit

which writes results data to the bdb. To couple this command to OMERO data, I don't want it to read or write data to a bdb, so I probably want to use a command more like

e2ctf.py 1.img --voltage=200 --apix=2 --cs=1 --autofit

from the web page above.

see also
http://blake.bcm.edu/emanwiki/EMAN2/CtfModel

Change History (10)

comment:1 Changed 14 years ago by wmoore

  • Description modified (diff)

comment:2 Changed 14 years ago by wmoore

  • Description modified (diff)

comment:3 Changed 14 years ago by wmoore

  • Status changed from new to assigned

comment:4 Changed 14 years ago by wmoore

  • Owner wmoore deleted
  • Status changed from assigned to new

comment:5 Changed 14 years ago by wmoore

  • Owner set to wmoore
  • Status changed from new to assigned

comment:6 Changed 14 years ago by wmoore

  • Description modified (diff)

comment:7 Changed 14 years ago by wmoore

  • Description modified (diff)

comment:8 Changed 14 years ago by wmoore

  • Description modified (diff)

comment:9 Changed 14 years ago by wmoore

Script added r6246.

comment:10 Changed 14 years ago by wmoore

  • Remaining Time changed from 2 to 0
  • Resolution set to fixed
  • Status changed from assigned to closed

(In [6249]) Additional CTF parameters. Closes #1844.

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