#!python

__author__ = 'SungHo Lee (shlee@unc.edu)'
__version_info__ = ('2017', '03', '25')
__version__ = '-'.join(__version_info__) + 'REV04'

import argparse, os
from pynit.handler.images import BrukerRawData


def main():
    parser = argparse.ArgumentParser(prog='brk2nifti', description="Convert Bruker raw data to Nifti formated image")
    parser.add_argument("pid", help="Proccessed ID (in case image is reconstructed)")
    parser.add_argument("path", help="Folder location for the Bruker raw data", type=str)
    parser.add_argument("filename", help="Filename w/o extension to export NifTi image", type=str)
    parser.add_argument("-V", "--version", action="version", version="%(prog)s ("+__version__+")")
    parser.add_argument("-o", "--orient", help="Reorientation to correct space", action='store_true', default=0)
    args = parser.parse_args()

    img = BrukerRawData(os.getcwd(), args.path, args.pid, ori=args.orient, convert=True)
    img.nii.to_filename('{}.nii.gz'.format(args.filename))

if __name__ == '__main__':
    main()