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 UploadIQMsInputSpec(BaseInterfaceInputSpec):
in_iqms = File(exists=True,
mandatory=True,
desc='the input IQMs-JSON file')
url = Str(mandatory=True, desc='URL (protocol and name) listening')
port = traits.Int(desc='MRIQCWebAPI service port')
path = Str(desc='MRIQCWebAPI endpoint root path')
email = Str(desc='set sender email')
strict = traits.Bool(False,
usedefault=True,
desc='crash if upload was not succesfull')
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 = traits.List(desc='BOLD functional series')
output_spaces = traits.List(desc='Target spaces')
template = traits.Enum('MNI152NLin2009cAsym', desc='Template space')
class ReadSidecarJSONOutputSpec(TraitedSpec):
subject_id = Str()
session_id = Str()
task_id = Str()
acq_id = Str()
rec_id = Str()
run_id = Str()
out_dict = traits.Dict()
class BIDSDataGrabberInputSpec(BaseInterfaceInputSpec):
subject_data = traits.Dict(Str, traits.Any)
subject_id = Str()
class SubjectSummaryOutputSpec(SummaryOutputSpec):
# This exists to ensure that the summary is run prior to the first ReconAll
# call, allowing a determination whether there is a pre-existing directory
subject_id = Str(desc='FreeSurfer subject ID')
class AboutSummaryInputSpec(BaseInterfaceInputSpec):
version = Str(desc='FMRIPREP version')
command = Str(desc='FMRIPREP command')
