def find_make_workdir(subdir, despike, spm, logger=None):
""" generates realign directory to query based on flags
and if it exists and create new workdir
"""
rlgn_dir = utils.defaults['realign_ants']
if spm:
rlgn_dir = utils.defaults['realign_spm']
if despike:
rlgn_dir = utils.defaults['despike'] + rlgn_dir
rlgn_dir = os.path.join(subdir, rlgn_dir)
if not os.path.isdir(rlgn_dir):
if logger:
logger.error('{0} doesnt exist skipping'.format(rlgn_dir))
raise IOError('{0} doesnt exist skipping'.format(rlgn_dir))
if logger:
logger.info(rlgn_dir)
workdirnme = utils.defaults['coreg']
workdir, exists = utils.make_dir(rlgn_dir, workdirnme)
if not exists:
if logger:
logger.error('{0}: skipping {1} doesnt exist'.format(subdir, workdir))
raise IOError('{0}: MISSING, Skipping'.format(workdir))
bpdirnme = utils.defaults['bandpass']
bpdir, exists = utils.make_dir(workdir, bpdirnme)
if exists:
if logger:
logger.error('{0}: skipping {1} existS'.format(subdir, bpdir))
raise IOError('{0}: EXISTS, Skipping'.format(bpdir))
return rlgn_dir, workdir, bpdir
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 find_make_workdir(subdir, despike, spm, gsr=False, logger=None):
""" generates realign directory to query based on flags
and if it exists and create new workdir
"""
rlgn_dir = utils.defaults['realign_ants']
if spm:
rlgn_dir = utils.defaults['realign_spm']
if despike:
rlgn_dir = utils.defaults['despike'] + rlgn_dir
rlgn_dir = os.path.join(subdir, rlgn_dir)
if not os.path.isdir(rlgn_dir):
if logger:
logger.error('{0} doesnt exist skipping'.format(rlgn_dir))
raise IOError('{0} doesnt exist skipping'.format(rlgn_dir))
if logger:
logger.info(rlgn_dir)
workdirnme = utils.defaults['coreg']
workdir, exists = utils.make_dir(rlgn_dir, workdirnme)
if not exists:
if logger:
logger.error('{0}: skipping {1} doesnt exist'.format(subdir, workdir))
raise IOError('{0}: MISSING, Skipping'.format(workdir))
bpdirnme = utils.defaults['bandpass']
bpdir, exists = utils.make_dir(workdir, bpdirnme)
if not exists:
if logger:
logger.error('{0}: skipping {1} exists'.format(subdir, bpdir))
raise IOError('{0}: Missing, Skipping'.format(bpdir))
modeldirnme = utils.defaults['model_fsl']
if gsr: # global signal regression
modeldirnme = modeldirnme + '_gsr'
modeldir, exists = utils.make_dir(bpdir, modeldirnme)
if not exists:
if logger:
logger.error('{0}: skipping {1} exists'.format(subdir, modeldir))
adjmatdir, exists = utils.make_dir(modeldir, 'adjacency_matrix')
if exists:
if logger:
logger.error('{0}: skipping {1} exists'.format(subdir, adjmatdir))
raise IOError('{0}: EXISTS, Skipping'.format(adjmatdir))
return rlgn_dir, workdir, bpdir, modeldir, adjmatdir
def process_subject(subdir, despike=False):
_, sid = os.path.split(subdir)
rawdir = os.path.join(subdir, "raw")
workdir = utils.defaults["realign_ants"]
if despike:
workdir = utils.defaults["despike"] + workdir
workdir, exists = utils.make_dir(subdir, workdir)
if exists:
raise IOError("{0}: skipping {1} exists".format(subdir, workdir))
funcs = split(rawdir, workdir, sid, despike)
aligned, move_arr = make_realign(funcs)
## Make aligned_4d
aligned4d = os.path.join(workdir, "align4d_{0}.nii.gz".format(sid))
aligned4d = utils.fsl_make4d(aligned, aligned4d)
print "aligned_4d:", aligned4d
plot_write_movement(workdir, sid, move_arr)
utils.zip_files(funcs)
utils.zip_files(aligned[1:])
print "{0} : finished".format(sid)
def process_subject(subdir, tr, logger, despike=False):
""" process one subject despike (optional), realign and
do slicetime correction via SPM tools"""
globstr = 'B*func4d.nii*'
workdirnme = utils.defaults['realign_spm']
if despike:
workdirnme = utils.defaults['despike'] + workdirnme
globstr = 'ds' + globstr
_, sid = os.path.split(subdir)
rawdir = os.path.join(subdir, 'raw')
workdir, exists = utils.make_dir(subdir, workdirnme)
if exists:
logger.error('{0}: skipping {1} exists'.format(subdir, workdir))
return None
funcs = split(rawdir, workdir, sid, logger, globstr)
if funcs is None:
logger.error('Raw dir missing data: {0}'.format(rawdir))
return None
staligned, move_arr = make_realignst(funcs, tr, logger)
if staligned is None:
return None
## Make aligned_4d
aligned4d = os.path.join(workdir, 'align4d_{0}.nii.gz'.format(sid))
aligned4d = utils.fsl_make4d(staligned, aligned4d)
logger.info(aligned4d)
## spm only has 6 params, add empty 7th for plotting
move_arr = np.hstack((move_arr,
np.zeros((move_arr.shape[0],1))))
plot_write_movement(workdir, sid, move_arr, logger)
## zip files
utils.zip_files(funcs)
utils.zip_files(staligned)
logger.info('{0} : finished'.format(sid))
