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 

Answer 2

Using skimage may be even easier after you installed SimpleITK

import skimage.io as io img = io.imread('file.mhd', plugin='simpleitk') 

This will give you a numpy array with z,y,x sorting.

Answer 3

Adding on the above posts, you can start with a CT-Scan .mhd file downloaded from the here and display / save 29 images with the following code (assuming that you have both the header and the raw files downloaded in the current directory):

import SimpleITK as sitk
import matplotlib.pylab as plt
ct_scans = sitk.GetArrayFromImage(sitk.ReadImage("training_001_ct.mhd", sitk.sitkFloat32))
plt.figure(figsize=(20,16))
plt.gray()
plt.subplots_adjust(0,0,1,1,0.01,0.01)
for i in range(ct_scans.shape[0]):
    plt.subplot(5,6,i+1), plt.imshow(ct_scans[i]), plt.axis('off')
    # use plt.savefig(...) here if you want to save the images as .jpg, e.g.,
plt.show()

Here is the same CT-scan .mhd file that is read with SimpleITK and animated: