import SimpleITK as sitk
import numpy as np
This funciton reads a '.mhd' file using SimpleITK and return the image array, origin and spacing of the image.
# Reads the image using SimpleITK
itkimage = sitk.ReadImage('C:/Users/tek/SampleNodule')
# Convert the image to a numpy array first and then shuffle the dimensions to get axis in the order z,y,x
ct_scan = sitk.GetArrayFromImage(itkimage)
# Read the origin of the ct_scan, will be used to convert the coordinates from world to voxel and vice versa.
origin = np.array(list(reversed(itkimage.GetOrigin())))
# Read the spacing along each dimension
spacing = np.array(list(reversed(itkimage.GetSpacing())))
return ct_scan, origin, spacing
# finally I am getting the following error and I can't fix it as i am novice for machine learing in python.
File "<ipython-input-4-5829076b62cd>", line 7
SyntaxError: invalid syntax