def average(fif,ave,projection="off",lowpass=40,highpass=0.0,gave=None): """ fif,ave are lists """ if "on" in proj: proja = True if "off" in proj: proja = False if len(fif) != len(ave): raise Exception("average:# fif != # ave") commands.process_raw(raw=fif,ave=ave,proj=proja,lowpass=lowpass,highpass=highpass,gave=gave_out)
def covariance(fif,cov,projection="off",lowpass=40,highpass=0.0,gcov=None): """ fif,ave are lists """ if "on" in proj: proja = True else: proja = False if len(fif) != len(cov): raise Exception("covariance:#fif != # ave") commands.process_raw(raw=fif,cov=cov,proj=proja,lowpass=lowpass,highpass=highpass,gcov=gcov)
def preProc(sub,directory,**kwargs): """ New pure-python pre-processing for MEG. kwargs:force """ #make folders dirs = ["raw_backup","eve","ave","cov","ave_projon","ave_projoff","ave_projon/logs","ave_projoff/logs"] for dir in dirs: to_make = os.path.join(directory,dir) if not os.path.exists(to_make): os.mkdir(to_make) raw_fifs = glob(os.path.join(directory,"*_raw.fif")) raw_fifs = filter(lambda x:not("Blink" in x or "emptyroom" in x),raw_fifs) #copy _raw.fif for raw in raw_fifs: fname = os.path.basename(raw) fname_copy = os.path.join(directory,"raw_backup",fname) if not os.path.exists(fname_copy): shutil.copyfile(raw,fname_copy) #extract events print("Extracting Events...") for raw in raw_fifs: eve_name = os.path.basename(raw).replace("_raw.fif",".eve") eve_p = os.path.join(directory,"eve",eve_name) result = commands.process_raw(raw=raw,eventsout=eve_p) if result: print("ERROR JUST OCCURED")
do_bhp = len(bhp_fif) == len(bhp_ave) ax_fif = sorted(glob(os.path.join(directory,"*AXCPT*_raw.fif"))) ax_ave = sorted(glob(os.path.join(directory,"ave","*AXCPT*.ave"))) do_ax = len(ax_fif) == len(ax_ave) #will need to fix later for single runs of AX for proj in ["projon","projoff"]: if proj == "projon": proj_arg = True else: proj_arg = False print("Projection:{0}".format(proj)) #ATLLoc gave = os.path.join(directory,"ave_proj"+proj,"{0}_ATLLoc-ave.fif".format(sub)) if do_atl: print("Averaging ATLLoc") commands.process_raw(raw=atl_fif,ave=atl_ave,proj=proj_arg,lowpass=20,highpass=0.5,gave=gave) #MaskedMM gave = os.path.join(directory,"ave_proj"+proj,"{0}_MaskedMM_All-ave.fif".format(sub)) if do_mask: print("Averaging Mask") commands.process_raw(raw=mask_fif,ave=mask_ave,proj=proj_arg,lowpass=20,gave=gave) #BaleenLP gave = os.path.join(directory,"ave_proj"+proj,"{0}_BaleenLP_All-ave.fif".format(sub)) if do_blp: print("Averaging BaleenLP") average(raw=blp_fif,ave=blp_ave,proj=proj_arg,lowpass=20,gave=gave) #BaleenHP gave = os.path.join(directory,"ave_proj"+proj,"{0}_BaleenHP_All-ave.fif".format(sub)) if do_bhp: print("Averaging BaleenHP") average(raw=blp_fif,ave=blp_ave,proj=proj_arg,lowpass=20,gave=gave)