enh/wip: adding subject to dmriprep-data

Author: akeshavan

dmriprep/cli.py

@@ -78,8 +78,26 @@ def main(participant_label, bids_dir, output_dir,
 @click.command()
 @click.argument('output_dir',
                 )
-def data(output_dir):
-    get_dataset(os.path.abspath(output_dir))
+@click.option('--subject', help="subject id to download (will choose 1 subject if not specified",
+              default="sub-NDARBA507GCT")
+@click.option('--study', help="which study to download. Right now we only support the HBN dataset",
+              default="HBN")
+def data(output_dir, study="HBN", subject="sub-NDARBA507GCT"):
+    """
+    Download dwi raw data in BIDS format from public datasets
+
+    :param output_dir: A directory to write files to
+    :param study: A study name, right now we only support 'HBN'
+    :param subject: A subject from the study, starting with 'sub-'
+    :return: None
+    """
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+
+    if study.upper() != 'HBN':
+        raise NotImplementedError('We only support data downloads from the HBN dataset right now.')
+
+    get_dataset(os.path.abspath(output_dir), source=study.upper(), subject_id=subject)
     print('done')
 
 

dmriprep/data.py

@@ -20,15 +20,14 @@
 mod_logger = logging.getLogger(__name__)
 
 
-def get_dataset(output_dir, source='HBN'):
+def get_dataset(output_dir, source='HBN', subject_id='sub-NDARBA507GCT'):
     if source in ['HBN']:
-        get_hbn_data(output_dir)
+        get_hbn_data(output_dir, subject_id)
     else:
         raise ValueError('Invalid dataset source')
 
 
-def get_hbn_data(output_dir):
-    subject_id = 'sub-NDARBA507GCT'
+def get_hbn_data(output_dir, subject_id):
     hbn_study = HBN(subjects=subject_id)
     subject = hbn_study.subjects[0]
     subject.download(directory=output_dir)