spark_bids.py 文件源码

def main():

    # Arguments parsing
    parser=argparse.ArgumentParser()

    # Required inputs
    parser.add_argument("bids_app_boutiques_descriptor", help="Boutiques descriptor of the BIDS App that will process the dataset.")
    parser.add_argument("bids_dataset", help="BIDS dataset to be processed.")
    parser.add_argument("output_dir", help="Output directory.")

    # Optional inputs
    parser.add_argument("--skip-participant-analysis", action = 'store_true', help="Skips participant analysis.")
    parser.add_argument("--skip-group-analysis", action = 'store_true', help="Skips groups analysis.")
    parser.add_argument("--skip-participants", metavar="FILE", type=lambda x: is_valid_file(parser, x), help="Skips participant labels in the text file.")
    parser.add_argument("--hdfs", action = 'store_true', help="Passes data by value rather than by reference in the pipeline. Use it with HDFS only. Requires HDFS to be started.")
    args=parser.parse_args()

    spark_bids = SparkBIDS(args.bids_app_boutiques_descriptor,
                           args.bids_dataset,
                           args.output_dir,
                           { 'use_hdfs': args.hdfs,
                             'skip_participant_analysis': args.skip_participant_analysis,
                             'skip_group_analysis': args.skip_group_analysis,
                             'skip_participants_file': args.skip_participants})

    sc = None

    if spark_bids.spark_required():
        # Spark initialization
        conf = SparkConf().setAppName("BIDS pipeline")
        sc = SparkContext(conf=conf)

    # Run!
    spark_bids.run(sc)

# Execute program