Merge pull request #2651 from effigies/fix/pybids_breakage

FIX: Various BIDSDataGrabber fixes

Author: effigies

nipype/interfaces/io.py

@@ -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):
@@ -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:
@@ -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 = {}

nipype/interfaces/tests/test_io.py

@@ -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,
@@ -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,