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.
Estimated time:
(Total: 0.00 h)
Description
Niko's request so that he can process the image stack of frames at will.
- 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.
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
- 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
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.
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.
- 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...
r16675 Adds correct runname, a report page and a link to the report page from the side menu panel.
- 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.
- Status changed from In Code Review to In Test
- Assignee changed from Jim Pulokas to Amber Herold
Looks like a simple and effective fix, now back to Amber as requested
r17525 matches changes in the directory where frames are saved.
- Status changed from In Test to Closed
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