From 5eeb072b11cd75dfa4a1931d83c4193cb4829fef Mon Sep 17 00:00:00 2001 From: Gaunab Date: Thu, 9 Dec 2021 16:59:59 +0100 Subject: [PATCH 1/3] add loading of saved layouts to BidsGrabber --- nipype/interfaces/io.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 142139548c..22fa4181b8 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -2866,6 +2866,7 @@ class BIDSDataGrabberInputSpec(DynamicTraitedSpec): output_query = traits.Dict( key_trait=Str, value_trait=traits.Dict, desc="Queries for outfield outputs" ) + load_layout = Directory(exists=True, desc="Path to load already saved Bidslayout.", mandatory=False) raise_on_empty = traits.Bool( True, usedefault=True, @@ -2965,9 +2966,13 @@ def __init__(self, infields=None, **kwargs): def _list_outputs(self): from bids import BIDSLayout - layout = BIDSLayout( - self.inputs.base_dir, derivatives=self.inputs.index_derivatives - ) + # if load_layout is given load layout which is on some datasets much faster + if isdefined(self.inputs.load_layout): + layout = BIDSLayout.load(self.inputs.load_layout) + else: + layout = BIDSLayout( + self.inputs.base_dir, derivatives=self.inputs.index_derivatives + ) if isdefined(self.inputs.extra_derivatives): layout.add_derivatives(self.inputs.extra_derivatives) From 4a33590ec7e629581946b802a7e2c78c54320997 Mon Sep 17 00:00:00 2001 From: Gaunab Date: Fri, 10 Dec 2021 09:58:32 +0100 Subject: [PATCH 2/3] added contribution name --- .zenodo.json | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.zenodo.json b/.zenodo.json index 4ac947b4a0..ee4f1c6a02 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -863,7 +863,13 @@ }, { "name": "Hui Qian, Tan" - } + }, + { + "affiliation": "Insitiute and Polyclinc for Diagnostic and Interventional Neuroradiology, University Hospital Carl Gustav Carus, Dresden, Germany", + "name": "Kuntke, Paul", + "orcid": "0000-0003-1838-2230" + } + ], "keywords": [ "neuroimaging", From 2ba8dacb8cc1f6f9c5b15b1cfb7b0395d45dcfb3 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Sat, 2 Apr 2022 12:49:15 -0400 Subject: [PATCH 3/3] STY/TEST: Make specs and run black [ignore-rev] --- nipype/interfaces/io.py | 4 +++- nipype/interfaces/tests/test_auto_BIDSDataGrabber.py | 3 +++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 22fa4181b8..78d8efc797 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -2866,7 +2866,9 @@ class BIDSDataGrabberInputSpec(DynamicTraitedSpec): output_query = traits.Dict( key_trait=Str, value_trait=traits.Dict, desc="Queries for outfield outputs" ) - load_layout = Directory(exists=True, desc="Path to load already saved Bidslayout.", mandatory=False) + load_layout = Directory( + exists=True, desc="Path to load already saved Bidslayout.", mandatory=False + ) raise_on_empty = traits.Bool( True, usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py index dd7d45e42b..c2a899958c 100644 --- a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py @@ -12,6 +12,9 @@ def test_BIDSDataGrabber_inputs(): mandatory=True, usedefault=True, ), + load_layout=dict( + mandatory=False, + ), output_query=dict(), raise_on_empty=dict( usedefault=True,