def _list_outputs(self):
# infields are mandatory, however I could not figure out how to set 'mandatory' flag dynamically
# hence manual check
if self._infields:
for key in self._infields:
value = getattr(self.inputs, key)
if not isdefined(value):
msg = "%s requires a value for input '%s' because it was listed in 'infields'" % \
(self.__class__.__name__, key)
outputs = {}
subject_id = self.inputs.subject_id
tp, group, pid = subject_id.split('_')
for key, args in self.inputs.template_args.items():
outputs[key] = []
template = self.inputs.template
if hasattr(self.inputs, 'field_template') and \
isdefined(self.inputs.field_template) and \
key in self.inputs.field_template:
template = self.inputs.field_template[key]
if isdefined(self.inputs.base_directory):
template = os.path.join(
os.path.abspath(self.inputs.base_directory), template)
else:
template = os.path.abspath(template)
if (('concatenated_fmri.nii.gz' not in template) and ('filled_t1' not in template)):
template = template % (tp, group, key, pid,
key, tp, pid)
elif 'concatenated_fmri.nii.gz' in template:
template = template % (tp, group, key, pid)
elif 'filled_t1' in template:
template = template %( tp, group, pid, tp,
group, pid, tp, pid)
filelist = glob.glob(template)
if len(filelist) == 0:
msg = 'output key: %s template: %s returned no files' % (
key, template)
if self.inputs.raise_on_empty:
raise IOError(msg)
else:
warn(msg)
else:
if self.inputs.sort_filelist:
filelist = human_order_sorted(filelist)
outputs[key] = list_to_filename(filelist)
if any([val is None for val in outputs[key]]):
outputs[key] = []
if len(outputs[key]) == 0:
outputs[key] = None
elif len(outputs[key]) == 1:
outputs[key] = outputs[key][0]
return outputs
def _list_outputs(self):
outputs = self._outputs().get()
pth = op.join(os.getcwd(), self.inputs.log_dir)
pes = human_order_sorted(glob(os.path.join(pth, "pe[0-9]*.*")))
assert len(pes) >= 1, "No pe volumes generated by FSL Estimate"
outputs["pes"] = pes
res4d = human_order_sorted(glob(os.path.join(pth, "res4d.*")))
assert len(res4d) == 1, "No residual volume generated by FSL Estimate"
outputs["res4d"] = res4d[0]
copes = human_order_sorted(glob(os.path.join(pth, "cope[0-9]*.*")))
assert len(copes) >= 1, "No cope volumes generated by FSL CEstimate"
outputs["copes"] = copes
var_copes = human_order_sorted(
glob(os.path.join(pth, "varcope[0-9]*.*")))
assert len(
var_copes) >= 1, "No varcope volumes generated by FSL CEstimate"
outputs["var_copes"] = var_copes
zstats = human_order_sorted(glob(os.path.join(pth, "zstat[0-9]*.*")))
assert len(zstats) >= 1, "No zstat volumes generated by FSL CEstimate"
outputs["zstats"] = zstats
if isdefined(self.inputs.f_con_file
) and self.inputs.f_con_file is not False:
zfstats = human_order_sorted(
glob(os.path.join(pth, "zfstat[0-9]*.*")))
assert len(
zfstats) >= 1, "No zfstat volumes generated by FSL CEstimate"
outputs["zfstats"] = zfstats
fstats = human_order_sorted(
glob(os.path.join(pth, "fstat[0-9]*.*")))
assert len(
fstats) >= 1, "No fstat volumes generated by FSL CEstimate"
outputs["fstats"] = fstats
tstats = human_order_sorted(glob(os.path.join(pth, "tstat[0-9]*.*")))
assert len(tstats) >= 1, "No tstat volumes generated by FSL CEstimate"
outputs["tstats"] = tstats
mrefs = human_order_sorted(
glob(os.path.join(pth, "mean_random_effects_var[0-9]*.*")))
assert len(
mrefs) >= 1, "No mean random effects volumes generated by FLAMEO"
outputs["mrefvars"] = mrefs
tdof = human_order_sorted(glob(os.path.join(pth, "tdof_t[0-9]*.*")))
assert len(tdof) >= 1, "No T dof volumes generated by FLAMEO"
outputs["tdof"] = tdof
weights = human_order_sorted(glob(os.path.join(pth,
"weights[0-9]*.*")))
assert len(weights) >= 1, "No weight volumes generated by FLAMEO"
outputs["weights"] = weights
outputs["stats_dir"] = pth
return outputs
def _list_outputs(self):
"""Find the files and expose them as interface outputs."""
outputs = {}
info = dict([(k, v) for k, v in list(self.inputs.__dict__.items())
if k in self._infields])
# check if the crumb is not absolute or if in info we have the parameter for the base directory
if not self._crumb.isabs():
first_arg_name, _ = self._crumb._first_open_arg()
if first_arg_name not in info:
raise KeyError(
'Crumb path is not absolute and could not find input for {}.'
.format(first_arg_name))
elif not op.isabs(info[first_arg_name]):
raise IOError(
'Expected an absolute path for {} argument in {} but got {}.'
.format(
first_arg_name,
self._crumb,
info[first_arg_name],
))
force_lists = self.inputs.force_lists
if isinstance(force_lists, bool):
force_lists = self._outfields if force_lists else []
bad_fields = set(force_lists) - set(self._outfields)
if bad_fields:
bad_fields = ", ".join(list(bad_fields))
plural = "s" if len(bad_fields) > 1 else ""
verb = "were" if len(bad_fields) > 1 else "was"
msg = ("The field%s '%s' %s set in 'force_lists' and not in "
"'templates'.") % (plural, bad_fields, verb)
raise ValueError(msg)
# loop over the crumb arguments to fill self_crumb
crumb_info = {
k: v
for k, v in info.items() if k in self._crumb.open_args()
}
ocrumb = self._crumb.replace(**crumb_info)
# check again if crumb path is absolute
if not ocrumb.isabs():
raise ValueError(
'Expected a Crumb with an absolute path, got {}.'.format(
ocrumb))
if not ocrumb.exists():
raise IOError(
'Expected an existing Crumb path, got {}.'.format(ocrumb))
# loop over all the ouput items and fill them with the info in templates
for field, template in self._templates.items():
# Fill in the template and glob for files
focrumb = ocrumb.replace(**dict(template))
if list(focrumb.open_args()):
raise ValueError(
'Expected a full specification of the Crumb path by now, got {}.'
.format(focrumb))
filelist = [cr.path for cr in focrumb.unfold()]
# Handle the case where nothing matched
if not filelist:
msg = "No files were found unfolding %s crumb path: %s" % (
field, focrumb)
if self.inputs.raise_on_empty:
raise IOError(msg)
else:
warn(msg)
# Possibly sort the list
if self.inputs.sort_filelist:
filelist = human_order_sorted(filelist)
# Handle whether this must be a list or not
if field not in force_lists:
filelist = list_to_filename(filelist)
outputs[field] = filelist
# add the crumb argument values for output
for arg_name in focrumb.all_args():
outputs[arg_name] = focrumb[arg_name][0]
return outputs
workflow.connect(sphere_left, "out_file", combine_left_right ,"in_file")
workflow.connect(sphere_right, "out_file", combine_left_right ,"operand_file")
datasink = pe.Node(nio.DataSink(), name='sinker')
datasink.inputs.base_directory = '/scr/ilz1/huntenburg/seed_connectivity/'
datasink.inputs.parameterization = True
workflow.connect(combine_left_right, 'out_file', datasink, 'roi')
subject_id_infosource = pe.Node(util.IdentityInterface(fields=["subject_id"]),
name="subject_id_infosource")
subjects = ['LEMON001']#,'LEMON006','LEMON087','LEMON030','LEMON044','LEMON071']
from nipype.utils.misc import human_order_sorted
subjects = human_order_sorted(subjects)
subject_id_infosource.iterables = ("subject_id", subjects)
templates={'epi_preproc':'kansas1/huntenburg/preproc/_cor_method_nonlin_ts/_subject_id_{subject_id}/bandpass_filter/nonlin_ts_detrended_regfilt_filt_300_masked.nii.gz',
'anat_brain':'jessica2/Schaare/LEMON/preprocessed/{subject_id}/freesurfer_anatomy/brain_out.nii.gz'
}
selectfiles = pe.Node(nio.SelectFiles(templates,
base_directory="/scr/"),
name="selectfiles")
workflow.connect(selectfiles, "anat_brain", sphere_left, "in_file_a")
def _list_outputs(self):
"""Find the files and expose them as interface outputs."""
outputs = {}
info = dict([(k, v) for k, v in list(self.inputs.__dict__.items())
if k in self._infields])
# check if the crumb is not absolute or if in info we have the parameter for the base directory
if not self._crumb.isabs():
first_arg_name, _ = self._crumb._first_open_arg()
if first_arg_name not in info:
raise KeyError('Crumb path is not absolute and could not find input for {}.'.format(first_arg_name))
elif not op.isabs(info[first_arg_name]):
raise IOError('Expected an absolute path for {} argument in {} but got {}.'.format(first_arg_name,
self._crumb,
info[first_arg_name],
))
force_lists = self.inputs.force_lists
if isinstance(force_lists, bool):
force_lists = self._outfields if force_lists else []
bad_fields = set(force_lists) - set(self._outfields)
if bad_fields:
bad_fields = ", ".join(list(bad_fields))
plural = "s" if len(bad_fields) > 1 else ""
verb = "were" if len(bad_fields) > 1 else "was"
msg = ("The field%s '%s' %s set in 'force_lists' and not in "
"'templates'.") % (plural, bad_fields, verb)
raise ValueError(msg)
# loop over the crumb arguments to fill self_crumb
crumb_info = {k: v for k, v in info.items() if k in self._crumb.open_args()}
ocrumb = self._crumb.replace(**crumb_info)
# check again if crumb path is absolute
if not ocrumb.isabs():
raise ValueError('Expected a Crumb with an absolute path, got {}.'.format(ocrumb))
if not ocrumb.exists():
raise IOError('Expected an existing Crumb path, got {}.'.format(ocrumb))
# loop over all the ouput items and fill them with the info in templates
for field, template in self._templates.items():
# Fill in the template and glob for files
focrumb = ocrumb.replace(**dict(template))
if list(focrumb.open_args()):
raise ValueError('Expected a full specification of the Crumb path by now, got {}.'.format(focrumb))
filelist = [cr.path for cr in focrumb.unfold()]
# Handle the case where nothing matched
if not filelist:
msg = "No files were found unfolding %s crumb path: %s" % (
field, focrumb)
if self.inputs.raise_on_empty:
raise IOError(msg)
else:
warn(msg)
# Possibly sort the list
if self.inputs.sort_filelist:
filelist = human_order_sorted(filelist)
# Handle whether this must be a list or not
if field not in force_lists:
filelist = list_to_filename(filelist)
outputs[field] = filelist
# add the crumb argument values for output
for arg_name in focrumb.all_args():
outputs[arg_name] = focrumb[arg_name][0]
return outputs
