Leginon

Beam tilt defocus calibration has been beam probe-dependent since 3.0 release. But we ourself don't switch that much. Is this switch within the same session ?

To double check if the last five defocus calibration are probe-dependent, try these python commands in your leginon environment, or look into your database with phpMyAdmin.

from leginon import leginondata
results = leginondata.MatrixCalibration(type='defocus').query(results=5)
for r in results:
  print r['probe']

I also thought that this was resolved in earlier versions as well.

Anyway, I did the test you suggested but I got an error:

>>> from leginon import leginondata
>>> results = leginondata.MatrixCalibration(type='defocus').query(results=5)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'MatrixCalibration

We are running myami/3.2.

Thanks,
Mike

Sorry,

The table is MatrixCalibrationData, not MatrixCalibration.

Therefore,

from leginon import leginondata
results = leginondata.MatrixCalibrationData(type='defocus').query(results=5)
for r in results:
  print r['probe']

Hi Anchi,

I finally checked the illumination setting and, yes, when I run the above commands I see nanoprobe or microprobe appropriately.

Despite this checking out OK, we still have a calibration problem. Essentially, despite seeing that the defocus calibration is appropriately assigned to a given present (depending on nanoprobe vs. microprobe), we are only able to focus correctly after doing the defocus calibration for a given setting.

To explain, here are the steps we follow:
1) Align microscope
2) Go to Calibrations application (v 3.3)
3) Load presets
4) Perform defocus calibration for 'fa' in Nanoprobe
5) Check Nanoprobe defocus measurement
6) Check Microprobe defocus measurement

What we see is that after calibrating for Nanoprobe, we are able to correctly focus in Nanoprobe. However, we lose the ability to focus using microprobe.

We also see that this problem is reversed if we do a microprobe defocus calibration and then check Nanoprobe focusing.

This means that we can only have one defocus calibration working at any given time.

Any thoughts on how we could further diagnose what is happening?

Thank you for your help!
mike

Hi, Michael,

Thanks for detailed report. See if this fix it :

In leginon/calibrationclient.py and in the function measureDefocusStig, Look for

    fmatrix = self.retrieveMatrix(tem, cam, 'defocus', ht, mag)

    probe = self.instrument.tem.ProbeMode
    fmatrix = self.retrieveMatrix(tem, cam, 'defocus', ht, mag, probe)

Looks like even though the probe is recorded but it was never used in the query part. If this fixes your problem, I will create a proper patch.

Thank you Anchi for the prompt response. That did it! We are now able to do use either imaging mode and the automated focusing works.

mike

Good to hear. Sorry about the bug.

Proper bug fix is handled in Issue #4894 and probe requirement extends to all beam tilt and focus related calibrations.