appion failed to generate frame stack
Added by Rui Zhang over 11 years ago
Hi, Anchi,
After switching from "image shift" to "modeled stage position" to move to targets between HM and SA, our leginon finally works! and I managed to collect some data.
Sorry I haven't tested the new script you sent me yet, but I'll let you know once I try it.
The new issue is our appion failed to generate frame stack. We have updated our appion to the trunk version and successfully ran the rawtransfer.py script. As a result, we have /k2data/frames/session/rawdata parallel to /k2data/leginon/session/rawdata.
The error message is attached. The division operation makes me think it has problem finding the gain reference.
| appion-trunk-fail (13.6 KB) appion-trunk-fail |
Replies (2)
RE: appion failed to generate frame stack - Added by Anchi Cheng over 11 years ago
Could you tell me the revision number that you updated the trunk version to? Did you update both linux and k2camera? The frame saving is done on k2 camera. If you are up to date, the new image saved should be in stack format, not singles. We changed that so that we can try out using gpu to do the gain correction part without extra step.
If you suspect it is having trouble finding the references. Try use getReferences.py attached here to see if combining the session path and reference image filename for a given image will give you an existing norm and dark mrc file. Run it with appion environment similar to makerawframestack.py and sinedon.cfg
| getReferences.py (1.41 KB) getReferences.py |
RE: appion failed to generate frame stack - Added by Anchi Cheng over 11 years ago
Also check your update procedure Gatan K2 Support Update of trunk from before 17514 to higher than 17561