upgrade to Leginon 3.5: Leginon moves twice as much
Added by Liang Tang almost 4 years ago
Hi, Anchi,
We are trying to upgrade the Leginon to version 3.5. After installation of new software, Leginon communicates well with scope and K3, and we can insert/withdraw grids, open/close column valve, etc. from Leginon GUI. But there is one interesting issue: Leginon seems to move as twice as it was. For example, when you went to the Navigator node and try to re-center to a feature (no matter if it is in sq, hl, en) by clicking on that feature, Leginon moved EXACTLY twice as much. Again this seems to happen in all mag/presets. Do you have any idea why this is happening? Maybe there is something in any .cfg file that needs to be modified? Btw, during Leginon upgrading, we didn't change any of .cfg files so the new Leginon uses the same .cfg files as the old version did before upgrading. Also, before upgrading, it worked well without any issue (pixel size calibration was done in the old version, but not in version 3.5).
I searched the wiki and found Bug #8160 but it might not be relevant.
Thanks in advance.
Liang
Replies (2)
RE: upgrade to Leginon 3.5: Leginon moves twice as much - Added by Anchi Cheng almost 4 years ago
Thanks for bringing up this issue. That is interesting.
I do think this is related to Bug #8160. You probably had 3.4 before that fix when you calibrated. You should reduce pixelsize calibration by half. However, Navigator should operate purely on the transformation matrix, so you are right that it does not make sense. No, there is no config change for this update. If it still does not work right, you may want to recalibrate or simply edit them. I can write a script.
If you use counting mode, is the binning=2 ?
RE: upgrade to Leginon 3.5: Leginon moves twice as much - Added by Liang Tang almost 4 years ago
Thanks, Anchi.
Yes binning is 2. Will try to modify pixel sizes in the calibration MSI.