def run_despike(datadir, globstr, taskid):
gstr = os.path.join(datadir, 'B*')
subjects = sorted(glob(gstr))
subdir = subjects[taskid]
_, sid = os.path.split(subdir)
rawdir, exists = utils.make_dir(subdir, 'raw')
if not exists:
return None
files, nfiles = utils.get_files(rawdir, 'ds*func*nii*')
if nfiles > 0:
print files, 'exists skipping'
return None
logger = logging.getLogger('despike')
logger.setLevel(logging.DEBUG)
ts = reg.timestr()
fname = os.path.split(__file__)[-1].replace('.py', '')
logfile = os.path.join(rawdir,
'{0}_{1}_{2}.log'.format(sid, fname, ts))
fh = logging.FileHandler(logfile)
fh.setLevel(logging.DEBUG)
logger.addHandler(fh)
logger.info(ts)
logger.info(__file__)
logger.info(os.getenv('USER'))
in4d = get_raw(rawdir, globstr, logger)
if in4d is None:
logger.error('in4d is None')
return
returncode, result = utils.afni_despike(in4d)
if returncode == 0:
logger.info('Despike finished')
logger.info(result.outputs.out_file)
return
logger.error(result.runtime.stderr)
def setup_logging(workdir, sid):
logger = logging.getLogger("bandpass")
logger.setLevel(logging.DEBUG)
ts = reg.timestr()
fname = os.path.split(__file__)[-1].replace(".py", "")
logfile = os.path.join(workdir, "{0}_{1}_{2}.log".format(sid, fname, ts))
fh = logging.FileHandler(logfile)
fh.setLevel(logging.DEBUG)
logger.addHandler(fh)
logger.info(__file__)
logger.info(ts)
logger.info(workdir)
logger.info(os.getenv("USER"))
return logger
def setup_logging(workdir, sid):
logger = logging.getLogger('fsl_model')
logger.setLevel(logging.DEBUG)
ts = reg.timestr()
fname = os.path.split(__file__)[-1].replace('.py', '')
logfile = os.path.join(workdir,
'{0}_{1}_{2}.log'.format(sid, fname, ts))
fh = logging.FileHandler(logfile)
fh.setLevel(logging.DEBUG)
logger.addHandler(fh)
logger.info(__file__)
logger.info(ts)
logger.info(workdir)
logger.info(os.getenv('USER'))
return logger
dest='globstr',
default='B*',
help='globstring to select subject directories ("B*")')
try:
args = parser.parse_args()
print args
except:
parser.print_help()
sys.exit()
datadir, tr = args.datadir, args.TR
globstr, despike = args.globstr, args.despike
logger = logging.getLogger('realignst_spm')
logger.setLevel(logging.DEBUG)
ts = reg.timestr()
fname = os.path.split(__file__)[-1].replace('.py', '')
logfile = os.path.join(datadir,
'logs',
'{0}_logger_{1}.log'.format(fname, ts))
fh = logging.FileHandler(logfile)
fh.setLevel(logging.DEBUG)
logger.addHandler(fh)
logger.info(os.getenv('USER'))
logger.info(ts)
logger.info(args)
#datadir, tr, despike = args.datadir, args.TR, args.despike
process_all(datadir, 'B*', tr, logger, despike)
#process_all(datadir, globstr, tr, logger, despike=False)
#process_all(datadir, 'B13*', repetition_time, logger, despike)
