Reading * .mhd / *. Raw format in python

Question

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

Answer 1

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

pip install SimpleITK 

works for many versions of python. 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 can be even easier after installing SimpleITK

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

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

Answer 3

Adding to the above messages, you can start with the CT-Scan.mhd file downloaded from here and display / save 29 images with the following code (provided that you have both the header and the raw files loaded). 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, eg, plt.show() 

Here is the same .mhd file for computed tomography, which is read using SimpleITK and animated:

Answer 4

You can try using MedPy or this mhd_utils script