Leginon

Matthias,

Please tell me what you get on these property calls

from pyscope import tia
t = tia.TIA_Falcon()
t.ccd.Camera
t.ccd.Name
r=t.ccd.PixelReadoutRange
r.StartX
r.StartY
r.EndX
r.EndY
t.ccd.GetTotalPixelReadoutRange.SizeY

By the way, I get these from pyscope tia.py, following what _getImage function has to do before it calls self.acqman.Acquire()

Since the version of the scripting except TUI is similar, I wonder if it does not switch camera properly and ends up trying to acquire with Orius which is smaller in dimension and thus failed. Jian's hint about TUI default camera might be in effect here. He observed that the default camera you get when TUI is started seems to be the only camera we can control through Leginon. It might be that our code does not truly switch camera properly when it comes to image acquisition and setup.

Matthias,

Is the SerialEM initialization done without Leginon opened and Application (such as Calibrations or Manual) loaded? Or has the Application has already opened and the camera can be found in Camera Settings of a node such as Correction node ?

Another way for me to understand this is if you can try the SerialEM "initialization" between these lines are issued as python commands on PC computer

from pyscope import tia
# Try initialize with SerialEM here
t = tia.TIA_Falcon()
# Try initialize with SerialEM here
t.selectSetup()
t.finalizeSetup()
# Try initialize with SerialEM here
t.acqman.Acquire()

Thanks.

Matthias's answer:

the SerialEM "initialization" was done without any leginon component running.

Matthias's test results:

### no SerialEM whatsoever:
>>> from pyscope import tia
>>> t = tia.TIA_Falcon()
>>> t.selectSetup()
>>> t.finalizeSetup()
>>> t.acqman.Acquire()
Traceback (most recent call last):
  File "<interactive input>", line 1, in <module>
  File "C:\Python27\lib\site-packages\comtypes\client\dynamic.py", line 42, in __call__
    return self._obj._comobj.Invoke(self._id, *args)
  File "C:\Python27\lib\site-packages\comtypes\automation.py", line 717, in Invoke
    raise COMError(hresult, text, details)
COMError: (-2147352567, 'Exception occurred.', (u'Cannot acquire with current acquisition setup', u'ESVision', None, 0L, 0))

### SerialEM after step 1:
>>> from pyscope import tia
>>> # started SerialEM here, took 1 Falcon image, exited SerialEM
>>> t = tia.TIA_Falcon()
>>> t.selectSetup()
>>> t.finalizeSetup()
>>> t.acqman.Acquire()
>>> # no error!

### SerialEM after step 2:
>>> from pyscope import tia
>>> t = tia.TIA_Falcon()
>>> # started SerialEM here, took 1 Falcon image, exited SerialEM
>>> t.selectSetup()
>>> t.finalizeSetup()
>>> t.acqman.Acquire()
>>> # no error!

### SerialEM after step 3:
>>> from pyscope import tia
>>> t = tia.TIA_Falcon()
>>> t.selectSetup()
>>> t.finalizeSetup()
>>> # started SerialEM here, took 1 Falcon image, exited SerialEM
>>> t.acqman.Acquire()
>>> # no error!

after "initializing" with serialem at step 3 (see below) in PythonWin on the scope PC ...

### SerialEM after step 3:
>>> from pyscope import tia
>>> t = tia.TIA_Falcon()
>>> t.selectSetup()
>>> t.finalizeSetup()
>>> # started SerialEM here, took 1 Falcon image, exited SerialEM
>>> t.acqman.Acquire()
>>> # no error!

... I left the PythonWin shell open on the PC and started the Leginon client on the PC and leginon host on Linux.
Then using manual acquisition I was still able to take a Falcon image on the Linux side and then a few more without any problems.

Then I closed Leginon host on Linux and leginon instrument client on PC.
After restarting leginon both on PC and Linux (the original PythonWin shell remained open and untouched), it produced the known error again upon acquisition on the Linux side.

Therefore, closing leginon (likely the PC instrument client) somehow undoes / resets the "SerialEM initialization".

I checked the status of the CCD camera buttons in TIA and the state in "TEM BlankerShutterMonitor" - there were no evident changes (camera retracted or the like) during all steps of these tests.

   Matthias

This is finally resolved with r18332 by setting ScanningServer to Spot mode before every image acquisition. Tested with remote session.

Matthias, please upload here the final tia.py file you are using so that I can make sure that I have not missed anything.

Hi Anchi,
sorry about taking my time. I will upload tia.py.

It works, but... Leginon cannot change cameras between Orius and Falcon. Could this be related to the spot-scan change we made in tia.py? I must change manually in the Titan UI.

M