class IQMFileSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
subject_id = Str(mandatory=True, desc='the subject id')
modality = Str(mandatory=True, desc='the qc type')
session_id = traits.Either(None, Str, usedefault=True)
task_id = traits.Either(None, Str, usedefault=True)
acq_id = traits.Either(None, Str, usedefault=True)
rec_id = traits.Either(None, Str, usedefault=True)
run_id = traits.Either(None, Str, usedefault=True)
metadata = traits.Dict()
provenance = traits.Dict()
root = traits.Dict(desc='output root dictionary')
out_dir = File(desc='the output directory')
_outputs = traits.Dict(value={}, usedefault=True)
def __setattr__(self, key, value):
if key not in self.copyable_trait_names():
if not isdefined(value):
super(IQMFileSinkInputSpec, self).__setattr__(key, value)
self._outputs[key] = value
else:
if key in self._outputs:
self._outputs[key] = value
super(IQMFileSinkInputSpec, self).__setattr__(key, value)
if key == 'subject_id':
#I can not find where it is set from bids ... dirty fix
if str(value) == '<undefined>':
self.subject_id = 'TODO'
class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
t1w = InputMultiPath(File(exists=True), desc='T1w structural images')
t2w = InputMultiPath(File(exists=True), desc='T2w structural images')
subjects_dir = Directory(desc='FreeSurfer subjects directory')
subject_id = Str(desc='Subject ID')
bold = InputMultiPath(traits.Either(File(exists=True),
traits.List(File(exists=True))),
desc='BOLD functional series')
output_spaces = traits.List(desc='Target spaces')
template = traits.Enum('MNI152NLin2009cAsym', desc='Template space')
class MaskEPIInputSpec(BaseInterfaceInputSpec):
in_files = InputMultiPath(File(exists=True),
mandatory=True,
desc='input EPI or list of files')
lower_cutoff = traits.Float(0.2, usedefault=True)
upper_cutoff = traits.Float(0.85, usedefault=True)
connected = traits.Bool(True, usedefault=True)
opening = traits.Int(2, usedefault=True)
exclude_zeros = traits.Bool(False, usedefault=True)
ensure_finite = traits.Bool(True, usedefault=True)
target_affine = traits.Either(None,
traits.File(exists=True),
default=None,
usedefault=True)
target_shape = traits.Either(None,
traits.File(exists=True),
default=None,
usedefault=True)
no_sanitize = traits.Bool(False, usedefault=True)
class UploadIQMsOutputSpec(TraitedSpec):
api_id = traits.Either(None,
traits.Str,
desc="Id for report returned by the web api")