Bug #2561
closedTomography stage tilt not reset after previous tilt-series aborted
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Description
SVN Version17944. Application:tomography
The tilt-series can be aborted during the middle of data collection, mostly due to low intensity or block of beam. However the stage tilt angle will stay as where was aborted. Then tomography still carry on to the next position, but with that tilted angle instead of 0 for navigation. The targeting will not be accurate due to stage tilt. The tilt-series will be collected at wrong places.
I notice such issue long time ago, and thought I reported it before.
Updated by Anchi Cheng about 11 years ago
I will look into this. I remember seeing codes that handles this.
Updated by Anchi Cheng about 11 years ago
- Status changed from New to Assigned
- Assignee changed from Anchi Cheng to Jian Shi
- Target version changed from Appion/Leginon 2.2.1 to Appion/Leginon 3.0.0
Jian,
I added extra code to restore original tilts when abort by instensity thredhold happens during the first half of the tilt but got enough to carry on the second half of the tilt series. However, the original tilt referes here is the tilt of the stage when tomography node starts its process. Therefore, if the stage was tilted when the targets were picked, it will return to that tilt when aborted or finishing successfully. The original code, even though lacking these extra code, would have gone to the same original tilt. Don't know if your original tilt was non-zero to start with when you observed this bug.
This change is r17988
If this still happens, please take a screen shot of tomography node logger window. I added a log that starts with "stage alpha reset to". I need to know what has happened around that log message.
Updated by Anchi Cheng about 11 years ago
- Project changed from Appion to Leginon
Updated by Sargis Dallakyan almost 7 years ago
- Status changed from Assigned to Closed