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FIX: Various BIDSDataGrabber fixes #2651

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Merged
merged 5 commits into from
Jul 25, 2018
Merged

FIX: Various BIDSDataGrabber fixes #2651

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1efa6cd
ENH: Exclude non-"proper" BIDS subdirectories
effigies Jul 25, 2018
db3b0ed
ENH: Add strict mode to BIDSDataGrabber
effigies Jul 25, 2018
4ab3437
FIX: BIDSDataGrabber indexing non-images
effigies Jul 25, 2018
b0b6670
TEST: More resilient tests
effigies Jul 25, 2018
799aacf
FIX: Dict syntax
effigies Jul 25, 2018
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13 changes: 10 additions & 3 deletions nipype/interfaces/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2755,6 +2755,8 @@ class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
desc='Generate exception if list is empty '
'for a given field')
return_type = traits.Enum('file', 'namedtuple', usedefault=True)
strict = traits.Bool(desc='Return only BIDS "proper" files (e.g., '
'ignore derivatives/, sourcedata/, etc.)')


class BIDSDataGrabber(IOBase):
Expand Down Expand Up @@ -2801,8 +2803,10 @@ def __init__(self, infields=None, **kwargs):
super(BIDSDataGrabber, self).__init__(**kwargs)

if not isdefined(self.inputs.output_query):
self.inputs.output_query = {"func": {"modality": "func"},
"anat": {"modality": "anat"}}
self.inputs.output_query = {
"func": {"modality": "func", 'extensions': ['nii', '.nii.gz']},
"anat": {"modality": "anat", 'extensions': ['nii', '.nii.gz']},
}

# If infields is empty, use all BIDS entities
if infields is None and have_pybids:
Expand All @@ -2828,7 +2832,10 @@ def _run_interface(self, runtime):
return runtime

def _list_outputs(self):
layout = gb.BIDSLayout(self.inputs.base_dir)
exclude = None
if self.inputs.strict:
exclude = ['derivatives/', 'code/', 'sourcedata/']
layout = gb.BIDSLayout(self.inputs.base_dir, exclude=exclude)

# If infield is not given nm input value, silently ignore
filters = {}
Expand Down
8 changes: 4 additions & 4 deletions nipype/interfaces/tests/test_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -592,9 +592,9 @@ def test_bids_grabber(tmpdir):
bg.inputs.base_dir = os.path.join(datadir, 'ds005')
bg.inputs.subject = '01'
results = bg.run()
assert os.path.basename(results.outputs.anat[0]) == 'sub-01_T1w.nii.gz'
assert os.path.basename(results.outputs.func[0]) == (
'sub-01_task-mixedgamblestask_run-01_bold.nii.gz')
assert 'sub-01_T1w.nii.gz' in map(os.path.basename, results.outputs.anat)
assert 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz' in \
map(os.path.basename, results.outputs.func)


@pytest.mark.skipif(not have_pybids,
Expand All @@ -610,7 +610,7 @@ def test_bids_fields(tmpdir):
bg.inputs.subject = '01'
bg.inputs.output_query['dwi'] = dict(modality='dwi')
results = bg.run()
assert os.path.basename(results.outputs.dwi[0]) == 'sub-01_dwi.nii.gz'
assert 'sub-01_dwi.nii.gz' in map(os.path.basename, results.outputs.dwi)


@pytest.mark.skipif(not have_pybids,
Expand Down