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)
