image shift target rotated by 90 degree between target selected in LM mode and exposure in SA mode
Added by Anchi Cheng over 10 years ago
From Maria Jansen:
It seems that the exposure and focus target that I set end up being 90 degrees off. I target specific features in the hl image, but when I check the hl image afterwards I can see the burn areas for exposure and focus targets being 90 degrees turned. I know there is a 90 degree rotation between 350x in LM and 4700 in SA mode on the scope. How do I correct for this?
Replies (6)
RE: image shift target rotated by 90 degree between target selected in LM mode and exposure in SA mode - Added by Anchi Cheng over 10 years ago
This is a bit hard to solve for general purpose because image shift axis definition changes in the transition of the two modes. However, here is a hack you can use. Replace leginon/presets.py with the attached file in your python site-package installation.
The function isLMtoSA at the moment check for the specific magnification you gave above. You may want to expand the range to your specific case.
The function specialTransform defines a matrix
m = numpy.matrix([[0,1],[-1,0]])
for a 90 degree clockwise rotation. You may need to try other rotation to match your case.
Give it a try.
| presets.py (64.3 KB) presets.py |
RE: image shift target rotated by 90 degree between target selected in LM mode and exposure in SA mode - Added by @Maria Janssen over 10 years ago
Thanks Anchi, I tried this but now Presets_Manager gives me an error: Image shift transform failed: unsupported operand type(s) for %: 'NoneType' and 'tuple'.
I can also not locate the burn holes in the general area where I should have seen exposure/focus burn holes.
RE: image shift target rotated by 90 degree between target selected in LM mode and exposure in SA mode - Added by @Maria Janssen over 10 years ago
Also, if this is going to be a big thing, I can wait until we have EFTEM installed in a couple of weeks. (Obviously, the objective aperture (70mm) is quickly in the way while z-focussing at this mag, or I have to decrease beam-tilt < 0.007 radians)
RE: image shift target rotated by 90 degree between target selected in LM mode and exposure in SA mode - Added by Anchi Cheng over 10 years ago
Sorry my typo in my fancy output.
Try this one.
| presets.py (64.3 KB) presets.py |
RE: image shift target rotated by 90 degree between target selected in LM mode and exposure in SA mode - Added by @Maria Janssen over 10 years ago
YES! Works great. Thanks Anchi!
RE: image shift target rotated by 90 degree between target selected in LM mode and exposure in SA mode - Added by Anchi Cheng almost 9 years ago
A note to all users:
I learned recently another case of this, also on a Polara microscope. The attached hack in the previous reply is for 3.0 version. Here I attach one good for 3.1
You will need to remove the -3.1 so that it is a proper python file. Check for the differences between that and what is currently in your installation. The change should be small.
| presets.py-3.1 (64.9 KB) presets.py-3.1 |