Leginon

The camera pixel number change should cause loss in ability in using old dark/bright images for gain correction, and presets, but not calibration, unless you somehow created new instrument.

Check with this python script on your leginon computer

from leginon import leginondata
cameras = leginondata.InstrumentData(name='GatanK2Counting').query()
for c in cameras:
  print c.dbid, c.timestamp.isoformat(), c['hostname']

This will give you the database record of the cameras that are named 'GatanK2Counting', when it was created, and the hostname. You should not get a new one when you changed the value in instruments.cfg. If you don't have a new one, your matrix and pixel calibration should still be good.

As for the gain/dark references, the easiest is just to retake them with the new geometry.

As for the presets, it indeed will cause the problem you had. We have seen that when we were learning how to get the orientation right. The first solution is to create brand new presets. The second solution is to modify the dimensions in the database after you import presets and before you try to use it, including trying to edit it. I will have to write a script for that or you will have a database person standby to modify the database record at that point. If you can do the first, it would be less work for me and less likely to go wrong : )

The software upgrade might also fix other things that we had to put in patches, such as the rotation of the raw frames, and not getting corrected offseted images. We don't have K2 now, so please let us know if you have noticed changes.

So I created new presets and see the calibratuions except the super resolution. Is is required to do that seperately? I also noticed that there are only 1x and 2x binnings now i.e. no 4x or 8x and center 1856,X1856 1X or 2X and center 3710.

Problem! I am getting the error now Acquisition failed CCD camera 'Gatan" not available. I restarted the client and leginon programs as welll as DM without success. I tried Super resolution as well as counted mode and can not get an image. Any thoughts?
Bob

This is bad, I don't know what Gatan changed to give you this problem of not getting images.

As for binning: 3710 / 4 = 927.5 Leginon detected that so it does not give you that as a common binning. Could you look up what camera configuration is available in DM?

With K2camera, you should expect seeing three cameras. We made each mode to be considered as a camera by Leginon. You should configure and find GatanK2Linear, GatanK2Counting, and GatanK2SuperResolution, not 'Gatan'. This also means different calibration for each.

The problem came when I changed the camera size in the instument.cfg I was getting images with it before I changed it but was worried it may mess things up. perhaps I should change it back and use custom size for the time being.

DM camera configuration has 1,2,3,4,5,6,7,8 binning binning 4 top -1, left -1, top 959 , bottom 927 to make it an even number

OK calibration for each.

I found the problem. My bad. I was trying to do a image shift calibration in the matrix node and did not have a camera selected and over ride was checked. All is well again. Thanks.