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Bug #7018

closed

Error in Python code when getting presets "From Scope"

Added by Amy Bondy about 5 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
-
Target version:
Start date:
03/22/2019
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.5
Show in known bugs:
No
Workaround:

Description

I had this issue start to arise in Leginon today. In the presets manager node when adjusting parameters (ie. intensity, image shift, beam shift) and pressing the "from scope" button, all the presets become grayed out and nothing further can be done in presets manager without restarting Leginon. This is the error I get in my terminal:

Exception in thread Thread-39:
Traceback (most recent call last):
File "/usr/lib64/python2.7/threading.py", line 812, in bootstrap_inner
self.run()
File "/usr/lib64/python2.7/threading.py", line 765, in run
self.__target(*self.__args, **self.__kwargs)
File "/lsi/cryoem_automation/myami/trunk/lib/python2.7/site-packages/leginon/presets.py", line 972, in fromScope
while trys < 3 and (newpreset['image shift']['x'] is None or newpreset['beam shift']['x'] is None or newpreset['diffraction shift']['x'] is None):
TypeError: 'NoneType' object has no attribute '__getitem
'

Actions #1

Updated by Anchi Cheng about 5 years ago

  • Status changed from New to In Test
  • Assignee set to Amy Bondy

It appears that you are using trunk version in which diffraction shift is added to the parameter to get and set in preset. Please update your microscope myami package to match the version. it should be fine after that. I may complain when you send preset the first time but will be o.k. afterwards.

Actions #2

Updated by Amy Bondy about 5 years ago

We tried updating the myami package however this did not seem to solve the issue. Instead when doing "from scope" in the presets manager, the same issue occurred (presets become grayed out and cannot send a preset to the scope unless you restart Leginon) plus an error message came up: "Preset change failed: unable to set instrument."

Actions #3

Updated by Anchi Cheng about 5 years ago

Was it the microscope that you updated the python code or the linux work station ? If you have tried both and still have trouble, I will need to help you directly.

Actions #4

Updated by Anchi Cheng about 5 years ago

Found out the issue is limited to trunk version. Still need to investigate.

Actions #5

Updated by Anchi Cheng over 3 years ago

  • Status changed from In Test to Closed
  • Target version set to Appion/Leginon 3.5
  • Affected Version changed from Appion/Leginon 3.4 to Appion/Leginon 3.5

tested with 3.4 database upgrade

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