rotateRPI2LPS.py

import numpy as np
import sys, os
import nrrd

if (len(sys.argv) < 2):
    print('Error: missing arguments!')
    print('e.g. python rotateRPI2LPS.py imageIn.nrrd [ImageOut.nrrd]')
    print('rotate RPI to LPS orientation for CMTK (as it doesn`t like RPI)')
else:
    print('Processing %s...'% (str(sys.argv[1])))
    data1, header1 = nrrd.read(str(sys.argv[1]))
    print(header1)
    header1['space'] = 'left-posterior-superior'
    header1.pop("space dimension", None)
    print(header1)
    data2 = np.flip(data1, (0, 2))
    print('saving...')
    if (len(sys.argv) == 3):
      nrrd.write(str(sys.argv[2]), data2, header1)
      print('saved to ' + str(sys.argv[2]))
    else:
      nrrd.write(str(sys.argv[1]).replace('.nrrd','_LPS.nrrd'), data2, header1)
      print('saved to ' + str(sys.argv[1]).replace('.nrrd','_LPS.nrrd'))