[ENH] Update BIDSDataGrabber for pybids 0.7

.travis.yml

@@ -86,8 +86,8 @@ before_install:
   fi;
 
 - travis_retry pip install -r requirements.txt
-- travis_retry pip install grabbit==0.1.2
-- travis_retry git clone -b 0.6.5 https://github.com/INCF/pybids.git ${HOME}/pybids && pip install -e ${HOME}/pybids
+- travis_retry pip install grabbit==0.2.6
+- travis_retry pip install git+https://github.com/bids-standard/pybids.git@0.7.0#egg=pybids
 
 install:
 - travis_retry pip install $EXTRA_PIP_FLAGS -e .[$NIPYPE_EXTRAS]

docker/generate_dockerfiles.sh

@@ -92,7 +92,7 @@ function generate_main_dockerfile() {
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
                                icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko
                                pandas psutil scikit-learn scipy traits=4.6.0' \
-                pip_install="grabbit==0.1.2 https://github.com/INCF/pybids/tarball/0.6.5" \
+                pip_install="grabbit==0.2.6 https://github.com/bids-standard/pybids/tarball/0.7.0" \
                 activate=true \
     --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
            docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \

nipype/info.py

@@ -169,7 +169,7 @@ def get_nipype_gitversion():
     'profiler': ['psutil>=5.0'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],
-    'pybids': ['pybids==0.6.5'],
+    'pybids': ['pybids==0.7.0'],
     'ssh': ['paramiko'],
     # 'mesh': ['mayavi']  # Enable when it works
 }

nipype/interfaces/io.py

@@ -2721,18 +2721,25 @@ def _list_outputs(self):
 
 
 class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
-    base_dir = Directory(exists=True,
-                         desc='Path to BIDS Directory.',
-                         mandatory=True)
-    output_query = traits.Dict(key_trait=Str,
-                               value_trait=traits.Dict,
-                               desc='Queries for outfield outputs')
-    raise_on_empty = traits.Bool(True, usedefault=True,
-                                 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.)')
+    base_dir = Directory(
+        exists=True,
+        desc='Path to BIDS Directory.',
+        mandatory=True)
+    output_query = traits.Dict(
+        key_trait=Str,
+        value_trait=traits.Dict,
+        desc='Queries for outfield outputs')
+    raise_on_empty = traits.Bool(
+        True, usedefault=True,
+        desc='Generate exception if list is empty for a given field')
+    return_type = traits.Enum(
+        'file', 'namedtuple', usedefault=True)
+    index_derivatives = traits.Bool(
+        False, usedefault=True,
+        desc='Index derivatives/ sub-directory')
+    extra_derivatives = traits.List(
+        Directory(exists=True),
+        desc='Additional derivative directories to index')
 
 
 class BIDSDataGrabber(LibraryBaseInterface, IOBase):
@@ -2758,10 +2765,10 @@ class BIDSDataGrabber(LibraryBaseInterface, IOBase):
     are filtered on common entities, which can be explicitly defined as
     infields.
 
-    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
+    >>> bg = BIDSDataGrabber(infields = ['subject'])
     >>> bg.inputs.base_dir = 'ds005/'
     >>> bg.inputs.subject = '01'
-    >>> bg.inputs.output_query['dwi'] = dict(modality='dwi')
+    >>> bg.inputs.output_query['dwi'] = dict(datatype='dwi')
     >>> results = bg.run() # doctest: +SKIP
 
     """
@@ -2781,18 +2788,17 @@ def __init__(self, infields=None, **kwargs):
 
         if not isdefined(self.inputs.output_query):
             self.inputs.output_query = {
-                "func": {"modality": "func", 'extensions': ['nii', '.nii.gz']},
-                "anat": {"modality": "anat", 'extensions': ['nii', '.nii.gz']},
+                "bold": {"datatype": "func", "suffix": "bold",
+                         "extensions": ["nii", ".nii.gz"]},
+                "T1w": {"datatype": "anat", "suffix": "T1w",
+                        "extensions": ["nii", ".nii.gz"]},
                 }
 
         # If infields is empty, use all BIDS entities
         if infields is None:
-            # Version resilience
-            try:
-                from bids import layout as bidslayout
-            except ImportError:
-                from bids import grabbids as bidslayout
-            bids_config = join(dirname(bidslayout.__file__), 'config', 'bids.json')
+            from bids import layout as bidslayout
+            bids_config = join(
+                dirname(bidslayout.__file__), 'config', 'bids.json')
             bids_config = json.load(open(bids_config, 'r'))
             infields = [i['name'] for i in bids_config['entities']]
 
@@ -2807,15 +2813,12 @@ def __init__(self, infields=None, **kwargs):
         self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
 
     def _list_outputs(self):
-        # Version resilience
-        try:
-            from bids import BIDSLayout
-        except ImportError:
-            from bids.grabbids import BIDSLayout
-        exclude = None
-        if self.inputs.strict:
-            exclude = ['derivatives/', 'code/', 'sourcedata/']
-        layout = BIDSLayout(self.inputs.base_dir, exclude=exclude)
+        from bids import BIDSLayout
+        layout = BIDSLayout(self.inputs.base_dir,
+                            derivatives=self.inputs.index_derivatives)
+
+        if isdefined(self.inputs.extra_derivatives):
+            layout.add_derivatives(self.inputs.extra_derivatives)
 
         # If infield is not given nm input value, silently ignore
         filters = {}

nipype/interfaces/tests/test_io.py

@@ -591,9 +591,9 @@ def test_bids_grabber(tmpdir):
     bg.inputs.base_dir = os.path.join(datadir, 'ds005')
     bg.inputs.subject = '01'
     results = bg.run()
-    assert 'sub-01_T1w.nii.gz' in map(os.path.basename, results.outputs.anat)
+    assert 'sub-01_T1w.nii.gz' in map(os.path.basename, results.outputs.T1w)
     assert 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz' in \
-        map(os.path.basename, results.outputs.func)
+        map(os.path.basename, results.outputs.bold)
 
 
 @pytest.mark.skipif(not have_pybids,
@@ -607,7 +607,7 @@ def test_bids_fields(tmpdir):
     bg = nio.BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
     bg.inputs.base_dir = os.path.join(datadir, 'ds005')
     bg.inputs.subject = '01'
-    bg.inputs.output_query['dwi'] = dict(modality='dwi')
+    bg.inputs.output_query['dwi'] = dict(datatype='dwi')
     results = bg.run()
     assert 'sub-01_dwi.nii.gz' in map(os.path.basename, results.outputs.dwi)
 
@@ -633,9 +633,9 @@ def test_bids_infields_outfields(tmpdir):
     for outfield in outfields:
         assert(outfield in bg._outputs().traits())
 
-    # now try without defining outfields, we should get anat and func for free
+    # now try without defining outfields
     bg = nio.BIDSDataGrabber()
-    for outfield in ['anat', 'func']:
+    for outfield in ['T1w', 'bold']:
         assert outfield in bg._outputs().traits()