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VNSautoRotator.py
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VNSautoRotator.py
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import numpy as np
import sys, os
import nrrd
if (len(sys.argv) < 2):
print('Error: missing arguments!')
print('e.g. python VNSautoRotator.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])))
ext = '_LPS'
data1, header1 = nrrd.read(str(sys.argv[1]))
print(header1)
header1['space'] = 'left-posterior-superior'
header1.pop("space dimension", None)
print(header1)
if (np.sum(np.sum(data1,(0,1))[-100:]) < np.sum(np.sum(data1,(0,1))[:100])):
print('RPI orientation detected so rotating to LPS...')
data2 = np.flip(data1, (0, 2))
data1 = data2
ext = '_RPI->LPS'
print('saving...')
if (len(sys.argv) == 3):
nrrd.write(str(sys.argv[2]), data1, header1)
print('saved to ' + str(sys.argv[2]))
else:
nrrd.write(str(sys.argv[1]).replace('.nrrd',ext + '.nrrd'), data1, header1)
print('saved to ' + str(sys.argv[1]).replace('.nrrd','_LPS.nrrd'))