ConvertLabels.py

import numpy as np
import sys
import nrrd

if (len(sys.argv) < 4):
    print('Error: missing arguments!')
    print('e.g. ConvertLabels.py [1,2,3,4,5] [5,4,3,2,1] imagefile.nrrd')
    print('e.g. ConvertLabels.py [1,2,3,4,5] [255,254,253,252,251] imagefile.nrrd optionaloutputfile.nrrd')
else:
     
    print('Changing label', str(sys.argv[1]), 'to', str(sys.argv[2]), 'for file', str(sys.argv[3]) )
    readdata, option = nrrd.read(str(sys.argv[3]))
    
    old_list = sys.argv[1].replace('[','').replace(']','').split(',')
    new_list = sys.argv[2].replace('[','').replace(']','').split(',')
    
    tempd = np.array(readdata)
    sm = readdata.size
    for i in range(0,len(new_list)):
        dc = readdata==np.uint8(old_list[i])
        tempd[dc] = np.uint8(new_list[i])
        print(old_list[i], '->', new_list[i], ' (', np.sum(dc), ')')
        sm = sm - np.sum(dc)
    print('Voxels not changed:', sm)
    
    if (len(sys.argv) < 5):
        print('saving result to', str(sys.argv[3]) )
    
        nrrd.write(str(sys.argv[3]), np.uint8(tempd), header=option)
    else:
        print('saving result to', str(sys.argv[4]) )
    
        nrrd.write(str(sys.argv[4]), np.uint8(tempd), header=option)
    
print('Done.')