TEM Scripting Beam Tilt Calibration
Added by Cheri Hampton over 13 years ago
We cannot locate get_beamtilt_scale.py
This is a suggested calibraion for our Tecni scope. Is it still necessary? Is the missing file going to cause a problem?
Cheri
Replies (3)
RE: TEM Scripting Beam Tilt Calibration - Added by Anchi Cheng over 13 years ago
You should find it under your myami/pyscope folder or in your python site-packages/pyscope folder if installed. You will do the calibration and use this script directly on your microscope computer. Have you updated your pyscope on the scope recently?
If you don't do it, you may need a fudge factor for all places where you use beam tilt (autofocus calibration and measurement etc.) to achieve the same accuracy these procedures are suppose to give. This is because if your Tecnai does need the scale factor, for example, 6, then when you input in Leginon to beam tilt by 0.01 radian, it will only do 0.0018 radian beam tilt.
Some people who saw the problem before we realized the cause simply scaled the input value, which is no problem, just have to remember that it is not in radian. Others used higher magnification to do autofocus to compensate for the inaccuracy. The latter is more problematic if you have significant hysteresis problem in mag changing.
RE: TEM Scripting Beam Tilt Calibration - Added by Cheri Hampton over 13 years ago
No, we haven't updated. The file is just not there.
Here is a list of files containing beamtilt
/usr/local/lib64/python2.6/site-packages/leginon/beamtiltimager.py
/usr/local/lib64/python2.6/site-packages/leginon/beamtiltimager.pyc
/usr/local/lib64/python2.6/site-packages/leginon/gui/wx/BeamTiltImager.pyc
/usr/local/lib64/python2.6/site-packages/leginon/gui/wx/BeamTiltFixer.pyc
/usr/local/lib64/python2.6/site-packages/leginon/gui/wx/BeamTiltImager.py
/usr/local/lib64/python2.6/site-packages/leginon/gui/wx/BeamTiltCalibrator.pyc
/usr/local/lib64/python2.6/site-packages/leginon/gui/wx/BeamTiltCalibrator.py
/usr/local/lib64/python2.6/site-packages/leginon/gui/wx/BeamTiltFixer.py
/usr/local/lib64/python2.6/site-packages/leginon/beamtiltcalibrator.pyc
/usr/local/lib64/python2.6/site-packages/leginon/beamtiltfixer.pyc
/usr/local/lib64/python2.6/site-packages/leginon/icons/beamtiltget.png
/usr/local/lib64/python2.6/site-packages/leginon/icons/beamtiltset.png
/usr/local/lib64/python2.6/site-packages/leginon/icons/beamtilt.png
/usr/local/lib64/python2.6/site-packages/leginon/beamtiltcalibrator.py
/usr/local/lib64/python2.6/site-packages/leginon/beamtiltfixer.py
Cheri
RE: TEM Scripting Beam Tilt Calibration - Added by Anchi Cheng over 13 years ago
Searching in Repository in redmine, it shows that I committed it to branch 2.0 on 2010-10-29 (svn revision r14974, 2.0.4 release) and to branch 2.1 (svn revision r14936, 2.1.1) on 2010-10.26. If you don't have the file in pyscope, yours is older than those dates. The documentation is updated when we make new bug fixes available. If you want to use this script, update to at least to one of these revision, if using svn, or release will give you the files. You should update within your branch if you do need new features, just critical bug fixes. They are the safest and least involved.