Leginon

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Gatan_K2_Installation_Notes

I belive we installed all the packages as listed in the page. Python hangs after the k.getImage() command.

Legion client starts up OK on the K2 computer.

Here is the output from Python:

C:\Users\Administrator>c:\Python27\python.exe
Python 2.7.3 (default, Apr 10 2012, 23:24:47) [MSC v.1500 64 bit (AMD64)] on win
32
Type "help", "copyright", "credits" or "license" for more information.

import pyscope.gatank2
k = pyscope.gatank2.GatanK2Counting()
k.setExposureTime(200)

k.getImage()

frame params: {'scaling': 1.0, 'filt': 'None', 'readMode': 1, 'alignFrames': Fa
lse, 'doseFrac': False, 'saveFrames': False, 'hardwareProc': 6, 'frameTime': 0.1
25}

We were able to create a preset in leginon but when trying to collect an image Leginon hung.
Leginon reports that it is acquiring a dose image.
K2 launcher reports: {'tcpport': 55555}
frame params: {'scaling': 1.0, 'filt': 'None', 'readMode': 1, 'alignFrames': Fa
lse, 'doseFrac': False, 'saveFrames': False, 'hardwareProc': 6, 'frameTime': 0.1
25}
DM reports in the output window:

SerialEMSocket: Function code not found: 23
SerialEMSocket: Function code not found: 25
0000000180890DC09963) - Aborted by user.
0000000180890DC010884) - Aborted by user.
SerialEMSocket: Function code not found: 23
SerialEMSocket: Function code not found: 25

I looked through the SerialEM plug-in code and found those missing function codes. They are the ones specific to K2, so I think the version of SerialEM plug-in you are using is before K2 support was introduced. Try the one I compiled here: https://emg.nysbc.org/attachments/download/1817/SEMCCD-GMS2-64.dll
That is what works on our K2. Or if you thought you were already using that one, then maybe there is still another one that is getting in the way somewhere else.
Jim

That is the one we are using We are also running serialEM from our Tecnai computer (not at the same time). Could there be a conflict there?

We got further by starting a completely new session but when trying to collect a dark reference we got the following communication error:
Traceback (most recent call last):
File "/usr/local/lib64/python2.6/site-packages/leginon/gui/wx/Corrector.py", line 230, in onSettingsTool
plan = self.node.retrieveCorrectorPlanFromSettings()
File "/usr/local/lib64/python2.6/site-packages/leginon/corrector.py", line 87, in retrieveCorrectorPlanFromSettings
cdata = self.instrument.getData(leginondata.CameraEMData)
File "/usr/local/lib64/python2.6/site-packages/leginon/instrument.py", line 256, in getData
raise results[i]
socket.error: [Errno 10053] An established connection was aborted by the software in your host machine
Exception in thread Thread-80:
Traceback (most recent call last):
File "/usr/lib64/python2.6/threading.py", line 522, in bootstrap_inner
self.run()
File "/usr/lib64/python2.6/threading.py", line 477, in run
self.__target(*self.__args, **self.__kwargs)
File "/usr/local/lib64/python2.6/site-packages/leginon/corrector.py", line 106, in acquireDark
imagedata = self.acquireReference(type='dark', channel=channel)
File "/usr/local/lib64/python2.6/site-packages/leginon/corrector.py", line 274, in acquireReference
refimagedata = self.acquireSeriesAverage(n, type, channel)
File "/usr/local/lib64/python2.6/site-packages/leginon/corrector.py", line 205, in acquireSeriesAverage
imagedata = self.acquireCameraImageData(type=exposuretype)
File "/usr/local/lib64/python2.6/site-packages/leginon/cameraclient.py", line 92, in acquireCameraImageData
imagedata['image'] = self.instrument.ccdcamera.Image
File "/usr/local/lib64/python2.6/site-packages/leginon/remotecall.py", line 220, in __getattr
return self._objectservice._call(self._nodename, self._name, name, 'r')
File "/usr/local/lib64/python2.6/site-packages/leginon/remotecall.py", line 354, in _call
return self.clients[node].send(request)
File "/usr/local/lib64/python2.6/site-packages/leginon/datatransport.py", line 62, in send
raise result
error: [Errno 10053] An established connection was aborted by the software in your host machine

I restarted Leginon and the K2 and Tecnai clients and repeated trying to get a dark reference. DM reported:
SerialEMSocket: Function code not found: 23
SerialEMSocket: Function code not found: 25
0000000180890DC09963) - Aborted by user.
0000000180890DC010884) - Aborted by user.
SerialEMSocket: Function code not found: 23
SerialEMSocket: Function code not found: 25
SerialEMSocket: Function code not found: 23
SerialEMSocket: Function code not found: 25

There appears to be a communication error with the camera.

With David Mastronarde's help we were able to track the socket error to running our current version of digital micrograph from a non standard location. This happened when Gatan was here "upgrading" our software. GMS was not "seeing" SEM-GMS2-64.dll. When it was placed in the prgramdata/gatan/plugin folder GMS was able to communicate properly. I was able to collect a gain reference image and will proceed with the rest of the calibrations tomorrow. Thanks.
Bob