Update output traits for BIDSDataGrabber

Author: mvdoc

nipype/interfaces/io.py

@@ -24,6 +24,7 @@
 import glob
 import fnmatch
 import string
+import json
 import os
 import os.path as op
 import shutil
@@ -2685,16 +2686,12 @@ class BIDSDataGrabber(IOBase):
     output_spec = DynamicTraitedSpec
     _always_run = True
 
-    def __init__(self, infields=None, outfields=None, **kwargs):
+    def __init__(self, infields=None, **kwargs):
         """
         Parameters
         ----------
         infields : list of str
             Indicates the input fields to be dynamically created
-
-        outfields: list of str
-            Indicates output fields to be dynamically created.
-            If no matching items, returns Undefined.
         """
         super(BIDSDataGrabber, self).__init__(**kwargs)
 
@@ -2707,12 +2704,8 @@ def __init__(self, infields=None, outfields=None, **kwargs):
             bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
             bids_config = json.load(open(bids_config, 'r'))
             infields = [i['name'] for i in bids_config['entities']]
-        # if outfields is not set, return those defined in infields
-        if infields and outfields is None:
-            outfields = [infield for infield in infields]
 
         self._infields = infields or []
-        self._outfields = outfields or []
 
         # used for mandatory inputs check
         undefined_traits = {}
@@ -2753,4 +2746,7 @@ def _list_outputs(self):
                     filelist = Undefined
 
             outputs[key] = filelist
-        return outputs
+        return outputs
+
+    def _add_output_traits(self, base):
+        return add_traits(base, list(self.inputs.output_query.keys()))

nipype/interfaces/tests/test_bids.py

@@ -9,14 +9,17 @@
 import glob
 import shutil
 import os.path as op
+import sys
 from subprocess import Popen
 import hashlib
 from collections import namedtuple
 
 import pytest
 import nipype
 import nipype.interfaces.io as nio
+from nipype.interfaces.base.traits_extension import isdefined
 from nipype.interfaces.base import Undefined
+from nipype.utils.filemanip import dist_is_editable
 
 # Check for boto
 noboto = False
@@ -43,6 +46,16 @@
 except CalledProcessError:
     fakes3 = False
 
+# check for bids
+have_pybids = True
+try:
+    import bids
+    from bids import grabbids as gb
+    filepath = os.path.realpath(os.path.dirname(bids.__file__))
+    datadir = os.path.realpath(os.path.join(filepath, 'grabbids/tests/data/'))
+except ImportError:
+    have_pybids = False
+
 
 def test_datagrabber():
     dg = nio.DataGrabber()
@@ -439,4 +452,63 @@ def test_jsonsink(tmpdir, inputs_attributes):
     assert data == expected_data
 
 
+# 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):
+    tmpdir.chdir()
+    bg = nio.BIDSDataGrabber()
+    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')
+
+
+@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')
+    results = bg.run()
+    assert os.path.basename(results.outputs.dwi[0]) == 'sub-01_dwi.nii.gz'
+
+
+@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_infields_outfields(tmpdir):
+    tmpdir.chdir()
+    infields = ['infield1', 'infield2']
+    outfields = ['outfield1', 'outfield2']
+    bg = nio.BIDSDataGrabber(infields=infields)
+    for outfield in outfields:
+        bg.inputs.output_query[outfield] = {'key': 'value'}
+
+    for infield in infields:
+        assert(infield in bg.inputs.traits())
+        assert(not(isdefined(bg.inputs.get()[infield])))
+
+    for outfield in outfields:
+        assert(outfield in bg._outputs().traits())
+
+    # now try without defining outfields, we should get anat and func for free
+    bg = nio.BIDSDataGrabber()
+    for outfield in ['anat', 'func']:
+        assert outfield in bg._outputs().traits()