Merge pull request #2737 from adelavega/update-pybids

[ENH] Update BIDSDataGrabber for pybids 0.7

Author: effigies

.travis.yml

@@ -89,8 +89,8 @@ 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 -e 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

@@ -107,7 +107,7 @@ function generate_main_dockerfile() {
     --user neuro \
     --miniconda use_env=neuro \
                 pip_opts="-e" \
-                pip_install="/src/nipype[all]" \
+                pip_install="/src/nipype[all] https://github.com/bids-standard/pybids/tarball/0.7.0" \
     --workdir /work \
     --label org.label-schema.build-date='$BUILD_DATE' \
             org.label-schema.name="NIPYPE" \

nipype/info.py

@@ -172,7 +172,7 @@ 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/fsl/tests/test_auto_EddyQuad.py

@@ -0,0 +1,65 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..epi import EddyQuad
+
+
+def test_EddyQuad_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        base_name=dict(
+            argstr='%s',
+            position=0,
+            usedefault=True,
+        ),
+        bval_file=dict(
+            argstr='--bvals=%s',
+            mandatory=True,
+        ),
+        bvec_file=dict(argstr='--bvecs=%s', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        field=dict(argstr='--field=%s', ),
+        idx_file=dict(
+            argstr='--eddyIdx=%s',
+            mandatory=True,
+        ),
+        mask_file=dict(
+            argstr='--mask=%s',
+            mandatory=True,
+        ),
+        output_dir=dict(
+            argstr='--output-dir=%s',
+            name_source=['base_name'],
+            name_template='%s.qc',
+        ),
+        output_type=dict(),
+        param_file=dict(
+            argstr='--eddyParams=%s',
+            mandatory=True,
+        ),
+        slice_spec=dict(argstr='--slspec=%s', ),
+        verbose=dict(argstr='--verbose', ),
+    )
+    inputs = EddyQuad.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_EddyQuad_outputs():
+    output_map = dict(
+        avg_b0_pe_png=dict(),
+        avg_b_png=dict(),
+        clean_volumes=dict(),
+        cnr_png=dict(),
+        qc_json=dict(),
+        qc_pdf=dict(),
+        residuals=dict(),
+        vdm_png=dict(),
+    )
+    outputs = EddyQuad.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/io.py

@@ -2721,18 +2721,23 @@ 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')
+    index_derivatives = traits.Bool(
+        False, mandatory=True, 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 +2763,10 @@ 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 +2786,17 @@ 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 +2811,12 @@ 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 = {}
@@ -2828,7 +2829,7 @@ def _list_outputs(self):
         for key, query in self.inputs.output_query.items():
             args = query.copy()
             args.update(filters)
-            filelist = layout.get(return_type=self.inputs.return_type, **args)
+            filelist = layout.get(return_type='file', **args)
             if len(filelist) == 0:
                 msg = 'Output key: %s returned no files' % key
                 if self.inputs.raise_on_empty:

nipype/interfaces/tests/test_auto_BIDSDataGrabber.py

@@ -6,10 +6,13 @@
 def test_BIDSDataGrabber_inputs():
     input_map = dict(
         base_dir=dict(mandatory=True, ),
+        extra_derivatives=dict(),
+        index_derivatives=dict(
+            mandatory=True,
+            usedefault=True,
+        ),
         output_query=dict(),
         raise_on_empty=dict(usedefault=True, ),
-        return_type=dict(usedefault=True, ),
-        strict=dict(),
     )
     inputs = BIDSDataGrabber.input_spec()
 

nipype/interfaces/tests/test_io.py

@@ -581,8 +581,6 @@ def test_jsonsink(tmpdir, inputs_attributes):
 # There are three reasons these tests will be skipped:
 @pytest.mark.skipif(not have_pybids,
                     reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
-                    reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
                     reason="Pybids is not installed in editable mode")
 def test_bids_grabber(tmpdir):
@@ -591,31 +589,27 @@ 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,
                     reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
-                    reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
                     reason="Pybids is not installed in editable mode")
 def test_bids_fields(tmpdir):
     tmpdir.chdir()
     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)
 
 
 @pytest.mark.skipif(not have_pybids,
                     reason="Pybids is not installed")
-@pytest.mark.skipif(sys.version_info < (3, 0),
-                    reason="Pybids no longer supports Python 2")
 @pytest.mark.skipif(not dist_is_editable('pybids'),
                     reason="Pybids is not installed in editable mode")
 def test_bids_infields_outfields(tmpdir):
@@ -633,9 +627,9 @@ 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()