Merge pull request #2174 from adelavega/bids_grabber

ENH: BIDS Data Grabber

Author: satra

.travis.yml

@@ -36,7 +36,12 @@ before_install:
   conda install python=${TRAVIS_PYTHON_VERSION} &&
   conda config --add channels conda-forge &&
   conda install -y nipype icu &&
-  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*; }
+  rm -r ${CONDA_HOME}/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype*;
+  pushd $HOME;
+  git clone https://github.com/INCF/pybids.git;
+  cd pybids;
+  pip install -e .;
+  popd; }
 #  Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi
 - travis_retry apt_inst
 - travis_retry conda_inst

.zenodo.json

@@ -528,6 +528,11 @@
       "affiliation": "Vrije Universiteit, Amsterdam",
       "name": "Gilles de Hollander",
       "orcid": "0000-0003-1988-5091"
+    },
+    {
+      "affiliation": "University of Texas at Austin",
+      "name": "De La Vega, Alejandro",
+      "orcid": "0000-0001-9062-3778"
     }
   ],
   "keywords": [

Dockerfile

@@ -87,6 +87,9 @@ COPY requirements.txt requirements.txt
 RUN pip install -r requirements.txt && \
     rm -rf ~/.cache/pip
 
+RUN git clone https://github.com/INCF/pybids.git && \
+    cd pybids && python setup.py develop
+
 # Installing nipype
 COPY . /src/nipype
 RUN cd /src/nipype && \

docker/base.Dockerfile

@@ -149,4 +149,3 @@ ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
     FORCE_SPMMCR=1
 
 WORKDIR /work
-

nipype/info.py

@@ -162,6 +162,7 @@ def get_nipype_gitversion():
     'profiler': ['psutil'],
     'duecredit': ['duecredit'],
     'xvfbwrapper': ['xvfbwrapper'],
+    'pybids' : ['pybids']
     # 'mesh': ['mayavi']  # Enable when it works
 }
 

nipype/interfaces/bids_utils.py

@@ -0,0 +1,169 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+""" Set of interfaces that allow interaction with BIDS data. Currently
+available interfaces are:
+
+BIDSDataGrabber: Query data from BIDS dataset using pybids grabbids.
+
+Change directory to provide relative paths for doctests
+>>> import os
+>>> import bids
+>>> filepath = os.path.realpath(os.path.dirname(bids.__file__))
+>>> datadir = os.path.realpath(os.path.join(filepath, 'grabbids/tests/data/'))
+>>> os.chdir(datadir)
+
+"""
+from os.path import join, dirname
+from .. import logging
+from .base import (traits,
+                   DynamicTraitedSpec,
+                   Directory,
+                   BaseInterface,
+                   isdefined,
+                   Str,
+                   Undefined)
+
+try:
+    from bids import grabbids as gb
+    import json
+except ImportError:
+    have_pybids = False
+else:
+    have_pybids = True
+
+LOGGER = logging.getLogger('workflows')
+
+class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
+    base_dir = Directory(exists=True,
+                         desc='Path to BIDS Directory.',
+                         mandatory=True)
+    output_query = traits.Dict(key_trait=Str,
+                               value_trait=traits.Dict,
+                               desc='Queries for outfield outputs')
+    raise_on_empty = traits.Bool(True, usedefault=True,
+                                 desc='Generate exception if list is empty '
+                                 'for a given field')
+    return_type = traits.Enum('file', 'namedtuple', usedefault=True)
+
+
+class BIDSDataGrabber(BaseInterface):
+
+    """ BIDS datagrabber module that wraps around pybids to allow arbitrary
+    querying of BIDS datasets.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.bids_utils import BIDSDataGrabber
+    >>> from os.path import basename
+
+    By default, the BIDSDataGrabber fetches anatomical and functional images
+    from a project, and makes BIDS entities (e.g. subject) available for
+    filtering outputs.
+
+    >>> bg = BIDSDataGrabber()
+    >>> bg.inputs.base_dir = 'ds005/'
+    >>> bg.inputs.subject = '01'
+    >>> results = bg.run()
+    >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_T1w.nii.gz'
+
+    >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+
+
+    Dynamically created, user-defined output fields can also be defined to
+    return different types of outputs from the same project. All outputs
+    are filtered on common entities, which can be explicitly defined as
+    infields.
+
+    >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['dwi'])
+    >>> bg.inputs.base_dir = 'ds005/'
+    >>> bg.inputs.subject = '01'
+    >>> bg.inputs.output_query['dwi'] = dict(modality='dwi')
+    >>> results = bg.run()
+    >>> basename(results.outputs.dwi[0]) # doctest: +ALLOW_UNICODE
+    'sub-01_dwi.nii.gz'
+
+    """
+    input_spec = BIDSDataGrabberInputSpec
+    output_spec = DynamicTraitedSpec
+    _always_run = True
+
+    def __init__(self, infields=None, outfields=None, **kwargs):
+        """
+        Parameters
+        ----------
+        infields : list of str
+            Indicates the input fields to be dynamically created
+
+        outfields: list of str
+            Indicates output fields to be dynamically created.
+            If no matching items, returns Undefined.
+        """
+        super(BIDSDataGrabber, self).__init__(**kwargs)
+        if not have_pybids:
+            raise ImportError("The BIDSEventsGrabber interface requires pybids."
+                              " Please make sure it is installed.")
+
+        # If outfields is None use anat and func as default
+        if outfields is None:
+            outfields = ['func', 'anat']
+            self.inputs.output_query = {
+                "func": {"modality": "func"},
+                "anat": {"modality": "anat"}}
+        else:
+            self.inputs.output_query = {}
+
+        # If infields is None, use all BIDS entities
+        if infields is None:
+            bids_config = join(dirname(gb.__file__), 'config', 'bids.json')
+            bids_config = json.load(open(bids_config, 'r'))
+            infields = [i['name'] for i in bids_config['entities']]
+
+        self._infields = infields
+        self._outfields = outfields
+
+        # used for mandatory inputs check
+        undefined_traits = {}
+        for key in infields:
+            self.inputs.add_trait(key, traits.Any)
+            undefined_traits[key] = Undefined
+
+        self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
+
+    def _run_interface(self, runtime):
+        return runtime
+
+    def _list_outputs(self):
+        layout = gb.BIDSLayout(self.inputs.base_dir)
+
+        for key in self._outfields:
+            if key not in self.inputs.output_query:
+                raise ValueError("Define query for all outputs")
+
+        # If infield is not given nm input value, silently ignore
+        filters = {}
+        for key in self._infields:
+            value = getattr(self.inputs, key)
+            if isdefined(value):
+                filters[key] = value
+
+        outputs = {}
+        for key, query in self.inputs.output_query.items():
+            args = query.copy()
+            args.update(filters)
+            filelist = layout.get(return_type=self.inputs.return_type,
+                                      **args)
+            if len(filelist) == 0:
+                msg = 'Output key: %s returned no files' % (
+                    key)
+                if self.inputs.raise_on_empty:
+                    raise IOError(msg)
+                else:
+                    LOGGER.warning(msg)
+                    filelist = Undefined
+
+            outputs[key] = filelist
+        return outputs

nipype/interfaces/io.py

@@ -40,6 +40,7 @@
 from .base import (
     TraitedSpec, traits, Str, File, Directory, BaseInterface, InputMultiPath,
     isdefined, OutputMultiPath, DynamicTraitedSpec, Undefined, BaseInterfaceInputSpec)
+from .bids_utils import BIDSDataGrabber
 
 try:
     import pyxnat