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[ENH] add option to include derivatives in BIDSDataGrabber #2815

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[ENH] add option to include derivatives in BIDSDataGrabber #2815

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b104679
[ENH] add option to include derivatives in BIDSDataGrabber
jdkent Dec 8, 2018
521e91a
add auto test and fix whitespace
jdkent Dec 8, 2018
8c5e20e
fix conflicts
jdkent Dec 9, 2018
90e2952
fix indent
jdkent Dec 9, 2018
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24 changes: 23 additions & 1 deletion nipype/interfaces/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
import tempfile
from os.path import join, dirname
from warnings import warn
from packaging import version

from .. import config, logging
from ..utils.filemanip import (
Expand Down Expand Up @@ -2733,6 +2734,10 @@ class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
return_type = traits.Enum('file', 'namedtuple', usedefault=True)
strict = traits.Bool(desc='Return only BIDS "proper" files (e.g., '
'ignore derivatives/, sourcedata/, etc.)')
domains = traits.Either(None, traits.List(),
usedefault=True,
desc='(Optional): Pass list of domains '
'(e.g. ["bids", "derivatives"]) for file searching.')


class BIDSDataGrabber(LibraryBaseInterface, IOBase):
Expand Down Expand Up @@ -2808,14 +2813,31 @@ def __init__(self, infields=None, **kwargs):

def _list_outputs(self):
# Version resilience
import bids
from packaging import version
try:
from bids import BIDSLayout
except ImportError:
from bids.grabbids import BIDSLayout

pybids_ver = version.parse(bids.__version__)
exclude = None
if self.inputs.strict:
exclude = ['derivatives/', 'code/', 'sourcedata/']
layout = BIDSLayout(self.inputs.base_dir, exclude=exclude)

if pybids_ver < version.parse('0.5'):
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@adelavega adelavega Dec 14, 2018 •
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Maybe you can include something like this in my PR? My PR is more general update to 0.7, and includes some extra functionality / updates, in addition to allowing for derivatives. I just hadn't merged because I'm waiting for pybids 0.7 release.

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@adelavega adelavega Dec 14, 2018 •
edited
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Although now that I think about it, I wouldn't worry too much about backwards compatibility. I would make 0.7 the hard requirement. The default behavior of my PR is to only look in the core BIDS folder, but you can optionally ask it to look in /derivatives or add extra paths.

raise ImportError("pybids must be >= 0.5, "
"installed version: {ver}".format(ver=pybids_ver))
elif pybids_ver >= version.parse('0.5') and pybids_ver < version.parse('0.6'):
layout = BIDSLayout(self.inputs.base_dir,
config=self.inputs.domains,
exclude=exclude)
else:
# pybids >= 0.6.0
if self.inputs.domains is None:
self.inputs.domains = ['bids']
layout = BIDSLayout((self.inputs.base_dir, self.inputs.domains),
exclude=exclude)

# If infield is not given nm input value, silently ignore
filters = {}
Expand Down
1 change: 1 addition & 0 deletions nipype/interfaces/tests/test_auto_BIDSDataGrabber.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
def test_BIDSDataGrabber_inputs():
input_map = dict(
base_dir=dict(mandatory=True, ),
domains=dict(usedefault=True, ),
output_query=dict(),
raise_on_empty=dict(usedefault=True, ),
return_type=dict(usedefault=True, ),
Expand Down