def get_raw(subdir, globstr, logger):
files, nfiles = utils.get_files(subdir, globstr)
logger.info('SUBID: {0}, nfiles: {1}'.format(subdir, nfiles))
if not nfiles == 1:
logger.error('Raw functional not found: {0}'.format(globstr))
return None
return files[0]
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 get_file(workdir, type_glob, logger=None):
files, nfiles = utils.get_files(workdir, type_glob)
## type_glob eg 'align4d_{0}.nii.gz'.format(sid) from utils.defaults)
if logger:
logger.info(' glob ({0}) yields nfiles: {1}'.format(type_glob, nfiles))
if nfiles == 1:
return files[0]
raise IOError('{0} in {1} not found'.format(type_glob, workdir))
def split(rawdir, destdir, sid, logger, globstr='B*func4d.nii*'):
""" split files into 3D vols,
return is None if it fails"""
files, nfiles = utils.get_files(rawdir, globstr)
logger.info('SUBID: {0}, nfiles: {1}'.format(sid, nfiles))
if not nfiles == 1:
logger.error('Raw functional not found: {0}'.format(globstr))
return None
rawfunc = files[0]
funcs = utils.fsl_split4d(rawfunc, destdir, sid)
return funcs
def split(rawdir, destdir, sid, despike=False):
globstr = "B*func4d.nii*"
if despike:
globstr = "ds" + globstr
files, nfiles = utils.get_files(rawdir, globstr)
if not nfiles == 1:
raise IOError("raw functional not found unexpected {0}".format(globstr))
rawfunc = files[0]
funcs = utils.fsl_split4d(rawfunc, destdir, sid)
if funcs is None:
raise IOError("splitting {0} failed".format(rawfunc))
return funcs