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FIX: Read BIDS config.json under grabbids or layout #2679

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Merged
merged 1 commit into from
Aug 10, 2018
Merged

FIX: Read BIDS config.json under grabbids or layout #2679

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12 changes: 9 additions & 3 deletions nipype/interfaces/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,10 +42,16 @@

have_pybids = True
try:
from bids import grabbids as gb
import bids
except ImportError:
have_pybids = False

if have_pybids:
try:
from bids import layout as bidslayout
except ImportError:
from bids import grabbids as bidslayout

try:
import pyxnat
except:
Expand Down Expand Up @@ -2810,7 +2816,7 @@ def __init__(self, infields=None, **kwargs):

# If infields is empty, use all BIDS entities
if infields is None and have_pybids:
bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
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']]

Expand All @@ -2835,7 +2841,7 @@ def _list_outputs(self):
exclude = None
if self.inputs.strict:
exclude = ['derivatives/', 'code/', 'sourcedata/']
layout = gb.BIDSLayout(self.inputs.base_dir, exclude=exclude)
layout = bidslayout.BIDSLayout(self.inputs.base_dir, exclude=exclude)

# If infield is not given nm input value, silently ignore
filters = {}
Expand Down
1 change: 0 additions & 1 deletion nipype/interfaces/tests/test_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,6 @@
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, 'tests/data/'))
except ImportError:
Expand Down