Merge pull request #31 from akeshavan/data_module

Data module

Author: akeshavan

dmriprep/cli.py

@@ -3,14 +3,51 @@
 """Console script for dmriprep."""
 import sys
 import click
+from . import run
+from . import io
+import os
 
 
 @click.command()
-def main(args=None):
-    """Console script for dmriprep."""
-    click.echo("Replace this message by putting your code into "
-               "dmriprep.cli.main")
-    click.echo("See click documentation at http://click.pocoo.org/")
+@click.option('--participant-label', help="The label(s) of the participant(s) that should be"
+                                           "analyzed. The label corresponds to"
+                                           "sub-<participant_label> from the BIDS spec (so it does"
+                                           "not include 'sub-'). If this parameter is not provided"
+                                           "all subjects will be analyzed. Multiple participants"
+                                           "can be specified with a space separated list.",
+              default=None
+              )
+@click.argument('bids_dir',
+                )
+@click.argument('output_dir',
+                )
+@click.argument('analysis_level',
+                type=click.Choice(['participant', 'group']),
+                default='participant')
+def main(participant_label, bids_dir, output_dir, analysis_level="participant"):
+    """
+    BIDS_DIR: The directory with the input dataset formatted according to the BIDS standard.
+
+    OUTPUT_DIR: The directory where the output files should be stored.
+    If you are running a group level analysis, this folder
+    should be prepopulated with the results of
+    the participant level analysis.
+
+    ANALYSIS_LEVEL: Level of the analysis that will be performed. Multiple
+    participant level analyses can be run independently
+    (in parallel).
+    """
+
+    if analysis_level is not 'participant':
+        raise NotImplementedError('The only valid analysis level for dmriprep is participant at the moment.')
+
+    inputs = io.get_BIDS_files(participant_label, bids_dir)
+
+    # for subject_id, subject_inputs in inputs:
+    #     run.run_dmriprep_pe(**subject_inputs,
+    #                         working_dir=os.path.join(output_dir, 'scratch'),
+    #                         out_dir=output_dir)
+    click.echo('doing stuff {} {} {} {}'.format(participant_label, bids_dir, output_dir, analysis_level))
     return 0