addPadding.py

import numpy as np
import sys, os
import nrrd

if (len(sys.argv) < 4):
    print('Error: missing arguments!')
    print('e.g. python addPadding.py #AddedSlicesLowEnd #AddedSlicesHighEnd imageIn.nrrd [imageOut.nrrd]')
else:
    Iin = str(sys.argv[3])
    print('Processing %s...'% (Iin))
    data1, header1 = nrrd.read(Iin)

    sh = np.shape(data1)

    Lpad = int(sys.argv[1])
    Hpad = int(sys.argv[2])

    data = np.zeros([sh[0],sh[1],sh[2]+Lpad+Hpad], dtype=np.uint8)
    data[0:sh[0],0:sh[1],Lpad:Lpad+sh[2]] = data1

    if (len(sys.argv) > 4):
      Iout = str(sys.argv[4])
      nrrd.write(Iout, data, options=header1)
      print('saved to ' + Iout)
    else:
      Iout = Iin.replace(".nrrd", "_" + str(sh[2]) + ".nrrd")
      nrrd.write(Iout, data1, options=header1)
      print('original saved to ' + Iout)
      nrrd.write(Iin, data, options=header1)
      print('padded version saved to ' + Iin)