def teardown(self, result=0):
"""
concatenate dtseries, parcellate, create grayplots.
:param result:
:return:
"""
fmris = [get_fmriname(fmri) for fmri in self.config.get_bids('func')]
fmrisets = list(
set([get_taskname(fmri) for fmri in self.config.get_bids('func')]))
script = self.script.format(**os.environ)
args = self.spec.format(**self.kwargs)
cmd = ' '.join((script, args))
cmd += ' --teardown'
for fmriset in fmrisets:
fmrilist = sorted([fmri for fmri in fmris if fmriset in fmri])
cmd += ' --tasklist ' + ','.join(fmrilist)
log_dir = self._get_log_dir()
out_log = os.path.join(log_dir,
self.__class__.__name__ + '_teardown.out')
err_log = os.path.join(log_dir,
self.__class__.__name__ + '_teardown.err')
result = self.call(cmd, out_log, err_log)
super(__class__, self).teardown(result)
def args(self):
for fmri in self.config.get_bids('func'):
# set ts parameters
self.kwargs['fmritcs'] = fmri
self.kwargs['fmriname'] = get_fmriname(fmri)
self.kwargs['fmriscout'] = None # not implemented
if self.kwargs['dcmethod'] == 'TOPUP':
self.kwargs['sephasepos'], self.kwargs['sephaseneg'] = \
self._get_intended_sefmaps()
else:
self.kwargs['sephasepos'] = self.kwargs['sephaseneg'] = None
# None to NONE
kw = {
k: (v if v is not None else "NONE")
for k, v in self.kwargs.items()
}
yield self.spec.format(**kw)
def get_tasklist(self):
"""
:return: dictionary of task basename: list of task names (with number)
"""
tasks = self.config.get_bids('func')
fmri_names = [get_fmriname(t) for t in tasks]
# filter out resting state data
pattern = re.compile(r'^((?!rest).)*$')
is_task = [pattern.match(t) is not None for t in fmri_names]
fmri_names = [t for i, t in enumerate(fmri_names) if is_task[i]]
task_names = list(
set(get_taskname(t) for i, t in enumerate(tasks) if is_task[i]))
task_dictionary = {}
for name in task_names:
task_dictionary[name] = [t for t in fmri_names if name in t]
return task_dictionary
def args(self):
for fmri, meta in zip(self.config.get_bids('func'),
self.config.get_bids('func_metadata')):
# set ts parameters
self.kwargs['fmritcs'] = fmri
self.kwargs['fmriname'] = get_fmriname(fmri)
self.kwargs['fmriscout'] = None # not implemented
if self.kwargs['dcmethod'] == 'TOPUP':
self.kwargs['seunwarpdir'] = ijk_to_xyz(
meta['PhaseEncodingDirection'])
self.kwargs['sephasepos'], self.kwargs['sephaseneg'] = \
self._get_intended_sefmaps()
else:
self.kwargs['sephasepos'] = self.kwargs['sephaseneg'] = None
# None to NONE
kw = {
k: (v if v is not None else "NONE")
for k, v in self.kwargs.items()
}
yield self.spec.format(**kw)
def args(self):
for fmri in self.config.get_bids('func'):
self.kwargs['fmriname'] = get_fmriname(fmri)
yield self.spec.format(**self.kwargs)