compressNRRD.py

import numpy as np
import sys
import os
import nrrd
import shutil

if (len(sys.argv) < 2):
    print('Error: missing arguments!')
    print('e.g. python compressNRRD.py imageIn.nrrd [ImageOut.nrrd]')
else:
    print('Processing %s...' % (str(sys.argv[1])))
    data1, header1 = nrrd.read(str(sys.argv[1]))
    print(header1)
    header1['encoding'] = 'gzip'
    if 'space directions' in header1.keys() and header1['space directions'] == ['none', 'none', 'none']:
        header1.pop("space directions", None)
    print(header1)
    print('saving...')
    if (len(sys.argv) == 3):
        nrrd.write(str(sys.argv[2]), data1, header1)
        print('saved to ' + str(sys.argv[2]))
    else:
        print('Creating temp backup (' +
              str(sys.argv[1]).replace('.nrrd', '_bk.nrrd') + ')')
        shutil.copy2(str(sys.argv[1]), str(
            sys.argv[1]).replace('.nrrd', '_bk.nrrd'))
        nrrd.write(str(sys.argv[1]), data1, header1)
        print('Removing temp backup...')
        os.remove(str(sys.argv[1]).replace('.nrrd', '_bk.nrrd'))
        print('saved to ' + str(sys.argv[1]))