binarize_fsl.py 文件源码

def main():

    conf = SparkConf().setAppName("binarize nifti")
    sc = SparkContext(conf=conf)
    sc.setLogLevel('ERROR')


    parser = argparse.ArgumentParser(description='Binarize images using FSL installed in a Docker container')
    parser.add_argument('threshold', type=int, help="binarization threshold")
    parser.add_argument('folder_path', type=str, help='folder path containing all of the splits')
    parser.add_argument('output_path', type=str, help='output folder path')

    args = parser.parse_args()

    print args.folder_path 
    client = Config().get_client('dev')

    nibRDD = sc.binaryFiles(args.folder_path)\
        .map(lambda x: get_data(x))\
        .map(lambda x: binarize(x, args.threshold))\
        .map(lambda x: copy_to_hdfs(x, args.output_path, client)).collect()