Feature #2496
closedswitching between nanoprobe,microprobe
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Description
function is in TEM scripting, need it in pyscope, leginon
Updated by Jim Pulokas over 11 years ago
- Status changed from Assigned to In Test
- Assignee changed from Jim Pulokas to Anchi Cheng
Anchi, I put functions getProbe and setProbe in tecnai.py in r17863. They are commented out until there is time to test.
usage is like: setProbe('micro') or setProbe('nano'). Likewise, the getProbe function will return either 'micro' or 'nano'.
ps. r17881 moved the constant lookup to init method. There is a screen recording of Jim working on this for the record
Updated by Anchi Cheng over 11 years ago
- Assignee changed from Anchi Cheng to Jian Shi
r17896 make probe mode selectable in presets manager and recorded in ScopeEMData
Jian,
Please test. You will need to update both pyscope and leginon on both microscope and your linux main. I have not aligned nanoprobe before here but the image and beam shift, however off, remain at the same position on TF20, so the switch seems to be stable. May have to adjust pause time in Exposure node.
Updated by Jian Shi over 11 years ago
I tested the nano/micro mode switch, seems every thing else were OK beside defocus. Say I have four presets:
sg 1700 microprobe -100um
hl 6500 microprobe -50um
fc 75000 nanoprobe 0um
en 75000 nanoprobe -1um
Whenever I switch from microprobe to nanoprobe (or vice verse), every thing else were set correctly, but defocus didn't change.
i.g 1) change from hl to fc, defocus will stay at -50um instead of 0.
Or 2) change from en sg, defocus will stay at -1um instead of -100um
However, if I resubmit the preset in the same mode, the defocus will be set correctly for the second time.
i.g. in case 1) I resubmit fc or en, the defocus will be correctly reset
in case 2) I resubmit sg or hl, the defocus will be correct.
I have not gotten time to test the beam-shift, image-shift, autofocus stuff yet, will update later
Thanks,
Jian
Updated by Anchi Cheng over 11 years ago
r17903 move probe mode setting to the front of all other scope parameters. This fixes the defocus problem which actually got set while still in the other mode.
Updated by Anchi Cheng over 11 years ago
nanoprobe and microprobe have different focus. Will need to be reset individually. Image shift can be used in both, suggesting magnification can be used in both.
Updated by Jian Shi over 11 years ago
It looks everything works fine now. Thanks.
Updated by Anchi Cheng about 11 years ago
r17916 makes Eucentric Focus, Rotation Center, and Defocus and Objective Stigmatiism calibration beam probe dependent so that nano probe and micro probe can have separate values at a given mag.
r17918 is the necessary database schema update so that old calibrations are not lost in the new query. This needs update on the microscope computer both in pyscope and in leginon.
Updated by Anchi Cheng about 11 years ago
- Status changed from In Test to Closed
- Target version set to myami-3.0
confirmed that it worked with Jian