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ENH: Enable filtering for ANY or NONE in --bids-filter-file #2123

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merged 7 commits into from
May 12, 2020
Merged

ENH: Enable filtering for ANY or NONE in --bids-filter-file #2123

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c9e5486
allow pybids none and any
bpinsard May 8, 2020
38189c0
add docs in the faq
bpinsard May 8, 2020
2eebfee
pep8
bpinsard May 8, 2020
0bb1253
using wildcard in json for pybids Query.ANY
bpinsard May 11, 2020
0059f00
remove null to Query.NONE, fix FAQ for wildcard instead of __any__
bpinsard May 11, 2020
3b44237
merge gh changes
bpinsard May 11, 2020
74c6980
use wildcard for pybids.layout.Query.ANY
bpinsard May 11, 2020
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4 changes: 3 additions & 1 deletion docs/faq.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -250,8 +250,10 @@ fMRIPrep uses the following queries, by default::
}

Only modifications of these queries will have any effect. You may filter on any entity defined
in the the PyBIDS
in the PyBIDS
`config file <https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json>`__.
To select images that do not have the entity set, use json value: ``null``.
To select images that have any non-empty value for an entity use string: ``'__any__'``

Can *fMRIPrep* continue to run after encountering an error?
-----------------------------------------------------------
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11 changes: 10 additions & 1 deletion fmriprep/cli/parser.py
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Expand Up @@ -40,10 +40,19 @@ def _drop_sub(value):
value = str(value)
return value.lstrip('sub-')

def _filter_pybids_none_any(dct):
import bids
for k, v in dct.items():
if v is None:
dct[k] = bids.layout.Query.NONE
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PyBIDS should already treat None like Query.None.

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Weird, I tried and it did not, and now it does.
Maybe my sleep deprived brain is just making a lot of typos. :/
I will remove it.

elif v == '__any__':
dct[k] = bids.layout.Query.ANY
return dct

def _bids_filter(value):
from json import loads
if value and Path(value).exists():
return loads(Path(value).read_text())
return loads(Path(value).read_text(), object_hook=_filter_pybids_none_any)

verstr = f'fMRIPrep v{config.environment.version}'
currentv = Version(config.environment.version)
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