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afanasyevp / afis

Aberration-free image shift (AFIS) compensation for the EPU data
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Problem with optics_add #1

Open hannahrbridges opened 4 years ago

hannahrbridges commented 4 years ago

Hi, I have tried using your AFIS scripts and the split one works nicely analysing the clusters, however with the optics_add script I keep getting the following error:

Traceback (most recent call last): File "optics_add.py", line 246, in main() File "optics_add.py", line 242, in main micrographs_write_optics(movies_filename, star_filename, str(args.o)) File "optics_add.py", line 144, in micrographs_write_optics OpticsFile_MainHeader, OpticsGroupData, OpticsHeader, MoviesData, StarFileType = star_analyze(OpticsFileName) File "optics_add.py", line 95, in star_analyze StarData[star_line[(_rlnMicrographMovieName_index-1)]]=star_line UnboundLocalError: local variable '_rlnMicrographMovieName_index' referenced before assignment

I have removed the optics group information from the input particle star file and the only place where this header '_rlnMicrographMovieName_index' occurs is in the output movies.star file from optics_split.py.

Any idea what could be going wrong?

Cheers! Hannah

afanasyevp commented 4 years ago

Hi Hannah,

Thanks for the feedback and I am sorry about this problem. Could you send me your star files (does not have to be the full) on pafanasyev[at]ethz.ch and I will try to fix the issue?

Cheers, Pavel

afanasyevp commented 4 years ago

Fixed