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avgMedImg.py
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avgMedImg.py
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'''
Target: avg for kinds of medical images, such as hdr, nii, mha, mhd, raw and so on, and store them as hdf5 files
Created on Oct. 20, 2016
Author: Dong Nie
'''
import SimpleITK as sitk
from multiprocessing import Pool
import os
import h5py
import numpy as np
def main():
path='./'
saveto='./'
datafilename='Brain_1to1_CT_resampled_from2to1.hdr' #provide a sample name of your filename of data here
datafn=os.path.join(path,datafilename)
imgOrg=sitk.ReadImage(datafn)
img1=sitk.GetArrayFromImage(imgOrg)
labelfilename='Brain_1to1_CT_resampled_from3to1.hdr' # provide a sample name of your filename of ground truth here
labelfn=os.path.join(path,labelfilename)
imgOrg=sitk.ReadImage(datafn)
img2=sitk.GetArrayFromImage(imgOrg)
labelfilename='Brain_1to1_CT_resampled_from4to1.hdr' # provide a sample name of your filename of ground truth here
labelfn=os.path.join(path,labelfilename)
imgOrg=sitk.ReadImage(datafn)
img3=sitk.GetArrayFromImage(imgOrg)
img=(img1+img2+img3)/3
volOut=sitk.GetImageFromArray(img)
sitk.WriteImage(volOut,'preSub1_MV.nii')
if __name__ == '__main__':
main()