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))
rcere = pp.find_single_file(globstr) 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)
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))
rcere = pp.find_single_file(globstr) 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)