Feature #1413
closedmake gain correction on dd raw frame mrc images into mrc stack
Added by Anchi Cheng about 13 years ago. Updated over 10 years ago.
100%
Description
Niko's request so that he can process the image stack of frames at will.
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.
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
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
Updated by Amber Herold over 12 years ago
- 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.
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.
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...
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.
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.
Updated by Jim Pulokas over 12 years ago
- 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
Updated by Anchi Cheng over 11 years ago
r17525 matches changes in the directory where frames are saved.
Updated by Amber Herold over 10 years ago
- Status changed from In Test to Closed