numpy - Reading *.mhd/*.raw format in python

Question

Can anyone please tell me the way I can read a dataset containing .mhd/.raw files in python?

Answer 1

The easiest way is to use SimpleITK (MedPy uses ITK for .mhd/.raw files too). Command

pip install SimpleITK

works for many python versions. For reading .mhd/.raw you can use this code from kaggle

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.
'''

def load_itk(filename):
    # Reads the image using SimpleITK
    itkimage = sitk.ReadImage(filename)

    # 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