the use of args.dir, args.basedir, and args.process in preprocess.py and the various processing scripts can be very confusing. the variable names should more explicitly refer to the particular directory being referred to. e.g.:
basedir: the bottom-level directory in which the processed data live (e.g. /data/brainsss/processed)
flydir: the base directory for a particular fly (e.g. /data/brainsss/processed/fly_001)
funcdir: a functional directory for a fly (e.g. /data/brainsss/processed/fly_001/func_0)
anatdir: an anatomy directory for a fly (e.g. /data/brainsss/processed/fly_001/anat_0)
because some steps can result in either a func or anat directory, we also need a term that can refer to this level of directory. it is currently referred to as args.process in preprocess.py, which seems like a confusing name. I propose args.datasubdir as that's somewhat more explicit.
the use of args.dir, args.basedir, and args.process in preprocess.py and the various processing scripts can be very confusing. the variable names should more explicitly refer to the particular directory being referred to. e.g.:
basedir: the bottom-level directory in which the processed data live (e.g. /data/brainsss/processed) flydir: the base directory for a particular fly (e.g. /data/brainsss/processed/fly_001) funcdir: a functional directory for a fly (e.g. /data/brainsss/processed/fly_001/func_0) anatdir: an anatomy directory for a fly (e.g. /data/brainsss/processed/fly_001/anat_0)
because some steps can result in either a func or anat directory, we also need a term that can refer to this level of directory. it is currently referred to as
args.processin preprocess.py, which seems like a confusing name. I proposeargs.datasubdiras that's somewhat more explicit.