Folder hierarchy not fully preserved for *_topazpicks.star #84
Description
I usually organize my cryo-EM data based on relion recommendations. See section 2.1 of Link.
For example, I put my tif files under Movies/10Feb2021 and import the movies into relion for the rest of the data analysis.
However, the relion wrapper of topaz only recognizes the last folder element in the hierarchy. In this case, 10Feb2021. This causes the picking result not able to display from relion gui.
The solution is to manually make a Movies folder under the External/jobXXX/ and move all the 10Feb2021/*_topazpicks.star files into it. However, it would be nice to recognize the folder hierarchy directly by the topaz wrapper.
This can be fixed by changing the following code
topaz/relion_run_topaz/run_topaz_pick.py
Line 96 in 617547c
to something like
os.system(str('''relion_star_printtable ''')+inargsMics+str(''' data_micrographs _rlnMicrographName | awk -F'job[0-9]*/' '{print $2}' | sed 's|/[^/]*.mrc||' > ''')+tmpfile)