logfile = os.path.join(root, "logs", "pib_%s%s.log" % (__file__, cleantime))
log_settings = pp.get_logging_configdict(logfile)
logging.config.dictConfig(log_settings)
tracer = "PIB"
user = os.environ["USER"]
logging.info("###START pib %s :::" % __file__)
logging.info("###TRACER %s :::" % (tracer))
logging.info("###USER : %s" % (user))
subs = bg.MyDirsDialog(prompt="Choose Subjects ", indir="%s/" % root)
for sub in subs:
print sub
globstr = os.path.join(sub, "raw", "*.v")
ecats = glob(globstr)
if len(ecats) < 1:
globstr = os.path.join(sub, "RawData", tracer, "*.v")
ecats = glob(globstr)
if len(ecats) < 1:
logging.error("%s missing, skipping" % (globstr))
continue
raw_ftimes = ft.frametimes_from_ecats(ecats)
ftimes = ft.frametimes_to_seconds(raw_ftimes)
timingf = ft.make_outfile(ecats[0])
ft.write_frametimes(ftimes, timingf)
logging.info("wrote %s" % (timingf))
ft_minutes = ft.frametimes_to_seconds(raw_ftimes, type="min")
sectimingf = ft.make_outfile(ecats[0], name="frametimes_in_minutes")
ft.write_frametimes(ft_minutes, sectimingf)
logging.info("wrote %s" % (sectimingf))
if rcere is None:
logging.error('%s missing, skipping'%(globstr))
continue
# get raw
globstr = os.path.join(sub, 'raw', '*.v')
ecats = glob(globstr)
if len(ecats) < 1:
globstr = os.path.join(sub, 'RawData', tracer, '*.v')
ecats = glob(globstr)
if len(ecats) < 1:
logging.error('%s missing, skipping'%(globstr))
continue
ftimes = ft.frametimes_from_ecats(ecats)
ftimes = ft.frametimes_to_seconds(ftimes)
timingf = ft.make_outfile(ecats[0])
ft.write_frametimes(ftimes, timingf)
k2ref = 0.15
range = (35,90)
logging.info('Running Logan')
dvrdir, exists = qa.make_qa_dir(pth, name='dvr')
if exists:
logging.warning('%s exists, remove to re-run'%(pth + '/dvr'))
continue
midtimes, durs = pyl.midframes_from_file(timingf)
data4d = pyl.get_data_nibabel(nifti)
ref = pyl.get_ref(rcere, data4d)
ref_fig = pyl.save_inputplot(ref, (midtimes + durs/2.), dvrdir)
masked_data, mask_roi = pyl.mask_data(rbrainmask, data4d)
x,y = pyl.calc_xy(ref, masked_data, midtimes)
allki, residuals = pyl.calc_ki(x, y, timingf, range=range)
log_settings = pp.get_logging_configdict(logfile)
logging.config.dictConfig(log_settings)
tracer = 'PIB'
user = os.environ['USER']
logging.info('###START pib %s :::'%__file__)
logging.info('###TRACER %s :::'%(tracer))
logging.info('###USER : %s'%(user))
subs = bg.MyDirsDialog(prompt='Choose Subjects ',
indir='%s/'%root)
for sub in subs:
print sub
globstr = os.path.join(sub, 'raw', '*.v')
ecats = glob(globstr)
if len(ecats) < 1:
globstr = os.path.join(sub, 'RawData', tracer, '*.v')
ecats = glob(globstr)
if len(ecats) < 1:
logging.error('%s missing, skipping'%(globstr))
continue
raw_ftimes = ft.frametimes_from_ecats(ecats)
ftimes = ft.frametimes_to_seconds(raw_ftimes)
timingf = ft.make_outfile(ecats[0])
ft.write_frametimes(ftimes, timingf)
logging.info('wrote %s'%(timingf))
ft_minutes = ft.frametimes_to_seconds(raw_ftimes, type='min')
sectimingf = ft.make_outfile(ecats[0], name = 'frametimes_in_minutes')
ft.write_frametimes(ft_minutes, sectimingf)
logging.info('wrote %s'%(sectimingf))
if rcere is None:
logging.error('%s missing, skipping' % (globstr))
continue
# get raw
globstr = os.path.join(sub, 'raw', '*.v')
ecats = glob(globstr)
if len(ecats) < 1:
globstr = os.path.join(sub, 'RawData', tracer, '*.v')
ecats = glob(globstr)
if len(ecats) < 1:
logging.error('%s missing, skipping' % (globstr))
continue
ftimes = ft.frametimes_from_ecats(ecats)
ftimes = ft.frametimes_to_seconds(ftimes)
timingf = ft.make_outfile(ecats[0])
ft.write_frametimes(ftimes, timingf)
k2ref = 0.15
range = (35, 90)
logging.info('Running Logan')
dvrdir, exists = qa.make_qa_dir(pth, name='dvr')
if exists:
logging.warning('%s exists, remove to re-run' % (pth + '/dvr'))
continue
midtimes, durs = pyl.midframes_from_file(timingf)
data4d = pyl.get_data_nibabel(nifti)
ref = pyl.get_ref(rcere, data4d)
ref_fig = pyl.save_inputplot(ref, (midtimes + durs / 2.), dvrdir)
masked_data, mask_roi = pyl.mask_data(rbrainmask, data4d)
x, y = pyl.calc_xy(ref, masked_data, midtimes)
allki, residuals = pyl.calc_ki(x, y, timingf, range=range)
