Added BIDSDataGrabber, test data and tests

Author: adelavega

nipype/interfaces/bids.py

@@ -0,0 +1,147 @@
+# -*- 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
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+    >>> os.chdir(datadir)
+
+"""
+
+from .base import (traits,
+                   DynamicTraitedSpec,
+                   BaseInterface,
+                   isdefined,
+                   Str,
+                   Undefined)
+
+from bids.grabbids import BIDSLayout
+
+
+class BIDSDataGrabberInputSpec(DynamicTraitedSpec):
+    base_dir = traits.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')
+    return_type = traits.Enum('filename', '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 import BIDSDataGrabber
+        >>> from os.path import basename
+        >>> import pprint
+
+        Select all files from a BIDS project
+
+        >>> bg = BIDSDataGrabber()
+        >>> bg.inputs.base_dir = 'ds005/'
+        >>> results = bg.run()
+        >>> pprint.pprint(len(results.outputs.outfield)) # doctest: +ALLOW_UNICODE
+        116
+
+        Using dynamically created, user-defined input fields,
+        filter files based on BIDS entities.
+
+        >>> bg = BIDSDataGrabber(infields = ['subject', 'run'])
+        >>> bg.inputs.base_dir = 'ds005/'
+        >>> bg.inputs.subject = '01'
+        >>> bg.inputs.run = '01'
+        >>> results = bg.run()
+        >>> basename(results.outputs.outfield[0]) # doctest: +ALLOW_UNICODE
+        'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+
+        Using user-defined output fields, return different types of outputs,
+        filtered on common entities
+        filter files based on BIDS entities.
+
+        >>> bg = BIDSDataGrabber(infields = ['subject'], outfields = ['func', 'anat'])
+        >>> bg.inputs.base_dir = 'ds005/'
+        >>> bg.inputs.subject = '01'
+        >>> bg.inputs.output_query['func'] = dict(modality='func')
+        >>> bg.inputs.output_query['anat'] = dict(modality='anat')
+        >>> results = bg.run()
+        >>> basename(results.outputs.func[0]) # doctest: +ALLOW_UNICODE
+        'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+
+        >>> basename(results.outputs.anat[0]) # doctest: +ALLOW_UNICODE
+        'sub-01_T1w.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 not outfields:
+            outfields = []
+        if not infields:
+            infields = []
+
+        super(BIDSDataGrabber, self).__init__(**kwargs)
+        undefined_traits = {}
+        # used for mandatory inputs check
+        self._infields = infields
+        self._outfields = outfields
+        for key in infields:
+            self.inputs.add_trait(key, traits.Any)
+            undefined_traits[key] = Undefined
+
+        if not isdefined(self.inputs.output_query):
+            self.inputs.output_query = {}
+
+        self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
+
+    def _run_interface(self, runtime):
+        return runtime
+
+    def _list_outputs(self):
+        if not self._outfields:
+            self._outfields = ['outfield']
+            self.inputs.output_query = {'outfield' : {}}
+        else:
+            for key in self._outfields:
+                if key not in self.inputs.output_query:
+                    raise ValueError("Define query for all outputs")
+
+        for key in self._infields:
+            value = getattr(self.inputs, key)
+            if not isdefined(value):
+                msg = "%s requires a value for input '%s' because" \
+                      " it was listed in 'infields'" % \
+                    (self.__class__.__name__, key)
+                raise ValueError(msg)
+
+        layout = BIDSLayout(self.inputs.base_dir)
+
+        filters = {i: getattr(self.inputs, i) for i in self._infields}
+
+        outputs = {}
+        for key, query in self.inputs.output_query.items():
+            outputs[key] = layout.get(
+                **dict(query.items() | filters.items()),
+                return_type='file')
+        return outputs

requirements.txt

@@ -13,4 +13,5 @@ configparser
 pytest>=3.0
 mock
 pydotplus
+pybids==0.3
 packaging