https://github.com/Radiomics/pyradiomics
Tip revision: 4775ee1fb88688ff64ca6bb747e49790da7f924d authored by Joost van Griethuysen on 05 July 2018, 14:01:01 UTC
v2.0.0 release
v2.0.0 release
Tip revision: 4775ee1
resampleMask.py
"""
This script is an example of how a mask image can be resampled to the geometry of a reference image. This enables the
a mask that has been generated on one image, to be used for feature extraction of another image. Please note that this
still requires the mask to have a similar physical space as the reference image.
This script can be used directly from the command line by calling ``python resampleMask.py <args>``, where <args> are
the reference image, mask to resample and a filename to store the result (the resampled mask).
"""
import argparse
import SimpleITK as sitk
parser = argparse.ArgumentParser()
parser.add_argument('image', metavar='Image', help='Reference image to resample the mask to')
parser.add_argument('mask', metavar='Mask', help='Input mask to resample')
parser.add_argument('resMask', metavar='Out', help='Filename to store resampled mask')
def main():
args = parser.parse_args()
image = sitk.ReadImage(args.image)
mask = sitk.ReadImage(args.mask)
rif = sitk.ResampleImageFilter()
rif.SetReferenceImage(image)
rif.SetOutputPixelType(mask.GetPixelID())
rif.SetInterpolator(sitk.sitkNearestNeighbor)
resMask = rif.Execute(mask)
sitk.WriteImage(resMask, args.resMask, True) # True enables compression when saving the resampled mask
if __name__ == '__main__':
main()