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FIX: Pybids grabbids API is going away
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nipype/interfaces/io.py

+8-3
Original file line numberDiff line numberDiff line change
@@ -42,10 +42,15 @@
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have_pybids = True
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try:
45-
from bids import grabbids as gb
45+
import bids
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except ImportError:
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have_pybids = False
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49+
try:
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from bids import layout as bidslayout
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except ImportError
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from bids import grabbids as bidslayout
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try:
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import pyxnat
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except:
@@ -2810,7 +2815,7 @@ def __init__(self, infields=None, **kwargs):
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# If infields is empty, use all BIDS entities
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if infields is None and have_pybids:
2813-
bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
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bids_config = join(dirname(bidslayout.__file__), 'config', 'bids.json')
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bids_config = json.load(open(bids_config, 'r'))
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infields = [i['name'] for i in bids_config['entities']]
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@@ -2835,7 +2840,7 @@ def _list_outputs(self):
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exclude = None
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if self.inputs.strict:
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exclude = ['derivatives/', 'code/', 'sourcedata/']
2838-
layout = gb.BIDSLayout(self.inputs.base_dir, exclude=exclude)
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layout = bidslayout.BIDSLayout(self.inputs.base_dir, exclude=exclude)
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# If infield is not given nm input value, silently ignore
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filters = {}

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