Merge pull request #143 from bpinsard/enh/bids_filter

ENH: Enable users to pass JSON filters to select subsets of data

setup.cfg

@@ -25,7 +25,7 @@ install_requires =
     matplotlib >= 2.2.0
     nibabel >= 3.0.1
     nipype >= 1.3.1
-    niworkflows ~= 1.1.6
+    niworkflows @ git+https://github.com/poldracklab/niworkflows.git@edeea81352f3f2b276f11e42e7829e1c5a03770f
     numpy
     packaging
     pybids ~= 0.9.4

smriprep/cli/run.py

@@ -51,6 +51,11 @@ def get_parser():
     g_bids.add_argument('--participant-label', '--participant_label', action='store', nargs='+',
                         help='a space delimited list of participant identifiers or a single '
                              'identifier (the sub- prefix can be removed)')
+    g_bids.add_argument(
+        '--bids-filter-file', action='store', type=Path, metavar='PATH',
+        help='a JSON file describing custom BIDS input filters using pybids '
+             '{<suffix>:{<entity>:<filter>,...},...} '
+             '(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)')
 
     g_perfm = parser.add_argument_group('Options to handle performance')
     g_perfm.add_argument('--nprocs', '--ncpus', '--nthreads', '--n_cpus', '-n-cpus',
@@ -270,6 +275,7 @@ def build_workflow(opts, retval):
     from subprocess import check_call, CalledProcessError, TimeoutExpired
     from pkg_resources import resource_filename as pkgrf
 
+    import json
     from bids import BIDSLayout
     from nipype import logging, config as ncfg
     from niworkflows.utils.bids import collect_participants
@@ -296,6 +302,8 @@ def build_workflow(opts, retval):
     subject_list = collect_participants(
         layout, participant_label=opts.participant_label)
 
+    bids_filters = json.loads(opts.bids_filter_file.read_text()) if opts.bids_filter_file else None
+
     # Load base plugin_settings from file if --use-plugin
     if opts.use_plugin is not None:
         from yaml import load as loadyml
@@ -412,6 +420,7 @@ def build_workflow(opts, retval):
         spaces=opts.output_spaces,
         subject_list=subject_list,
         work_dir=str(work_dir),
+        bids_filters=bids_filters,
     )
     retval['return_code'] = 0
 

smriprep/workflows/base.py

@@ -38,6 +38,7 @@ def init_smriprep_wf(
     spaces,
     subject_list,
     work_dir,
+    bids_filters,
 ):
     """
     Create the execution graph of *sMRIPrep*, with a sub-workflow for each subject.
@@ -72,6 +73,7 @@ def init_smriprep_wf(
                 spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
                 subject_list=['smripreptest'],
                 work_dir='.',
+                bids_filters=None,
             )
 
     Parameters
@@ -109,6 +111,9 @@ def init_smriprep_wf(
     work_dir : :obj:`str`
         Directory in which to store workflow execution state and
         temporary files
+    bids_filters : dict
+        Provides finer specification of the pipeline input files through pybids entities filters.
+        A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
 
     """
     smriprep_wf = Workflow(name='smriprep_wf')
@@ -141,6 +146,7 @@ def init_smriprep_wf(
             skull_strip_template=skull_strip_template,
             spaces=spaces,
             subject_id=subject_id,
+            bids_filters=bids_filters,
         )
 
         single_subject_wf.config['execution']['crashdump_dir'] = (
@@ -172,6 +178,7 @@ def init_single_subject_wf(
     skull_strip_template,
     spaces,
     subject_id,
+    bids_filters,
 ):
     """
     Create a single subject workflow.
@@ -209,6 +216,7 @@ def init_single_subject_wf(
                 skull_strip_template=Reference('OASIS30ANTs'),
                 spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
                 subject_id='test',
+                bids_filters=None,
             )
 
     Parameters
@@ -243,6 +251,9 @@ def init_single_subject_wf(
         Object containing standard and nonstandard space specifications.
     subject_id : :obj:`str`
         List of subject labels
+    bids_filters : dict
+        Provides finer specification of the pipeline input files through pybids entities filters.
+        A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
 
     Inputs
     ------
@@ -257,7 +268,7 @@ def init_single_subject_wf(
             't1w': ['/completely/made/up/path/sub-01_T1w.nii.gz'],
         }
     else:
-        subject_data = collect_data(layout, subject_id)[0]
+        subject_data = collect_data(layout, subject_id, bids_filters=bids_filters)[0]
 
     if not subject_data['t1w']:
         raise Exception("No T1w images found for participant {}. "