Task #1844 (closed)
Opened 14 years ago
Closed 14 years ago
CTF correction by EMAN2
Reported by: | wmoore | Owned by: | wmoore |
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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 |
Sprint: | n.a. |
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.
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
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
Script added r6246.