Bug #4246
closed
Filament is turned off between images on JEOL 1400
Added by Neil Voss over 8 years ago.
Updated almost 7 years ago.
Affected Version:
Appion/Leginon 3.2
Description
the filament is shut off whenever an image is taken, no matter if it’s in corresponding node (z-focus, focus exposure, etc) or navigation. This happened immediately when the message “Open Column Valve for camera exposure...” pop in the log as below.
We just upgraded to Leginon 3.2, we have a JEOL 1400 with a Gatan 4k UltraScan. We are running the jeolcom and dmsem pyscope module for controlling the scope.
Does this happen even though the valve is already opened ?
Try a direct call that opens beam valve on scope computer in python command line
from pyscope import jeolcom
j = jeolcom.Jeol()
j.setColumnValvePosition('open')
This function calls feg3 in jeol scripting which 1400 model might not have.
If it is true, we can detect and avoid it.
The 1400 of ours does not have a column valve.
try it any way. I want to know if that is what I need to create a condition for or something else that does not show in the log.
Two things leginon does in 3.2 that not done previously before an acquisition are setColumnValvePosition('open'), and setBeamBlank('off').
filament off
run j.setColumnValvePosition('open')
turns filament on
(wait for full voltage)
run j.setColumnValvePosition('open')
turns filament off
(wait for voltage off)
run j.setColumnValvePosition('closed')
turns filament on
(no wait, not charged)
run j.setColumnValvePosition('closed')
nothing happens, filament is still on
beam is on
setBeamBlank('off')
nothing happens
setBeamBlank('on')
beam goes away
setBeamBlank('off')
beam is restored
Made a change locally to jeolcom.py to disable function, maybe we should move this to jeol.cfg:
def setColumnValvePosition(self, position):
return
if position == 'open':
self.feg3.SetBeamValve(1)
elif position == 'closed':
self.feg3.SetBeamValve(0)
else:
raise ValueError
Peculiar. It is turning filament on and off on each call regardless of the state.
I will make changes to have this in the jeol.cfg
- Status changed from Assigned to In Test
- Assignee changed from Anchi Cheng to Neil Voss
- Target version set to Appion/Leginon 3.2
r19879 fix in trunk r19880 fix in 3.2
- Status changed from In Test to Closed
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