Range indexing an ITK image by variables

Engineering
,
1

I’m trying to slice an sitk image in 3D but having trouble. The following code doesn’t work for some reason

Does not work

image = sitk.ReadImage('./myImage.nrrd')

i_indices = np.arange(100,164) // or range(100,164)
j_indices = np.arange(100,164)
z_indices = 100

image[i_indices, j_indices, z_indices]

Works

image[100:164, 100:164, 100]

The error is

~/.../python3.8/site-packages/SimpleITK/SimpleITK.py in __getitem__(self, idx)
   4139             idx = (idx, Ellipsis)
   4140 
-> 4141         if len(idx) > dim + (Ellipsis in idx):
   4142           raise IndexError("too many indices for image")
   4143         if (len(idx) < dim) and Ellipsis not in idx:

ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

I tried np.ix_ approach in numpy too but no success.

How can I not go to Array (sitk.GetArrayFromImage), and still be able to slice a range in sitk image by indexing via variables? I think I’m missing something obvious but googling for a good amount of time didn’t result in a solution.

Thanks

2

Hello @sedghi,

SimpleITK does not support that type for indexing. You can use slice:

import SimpleITK as sitk

image = sitk.ReadImage('./myImage.nrrd')

i_indices = slice(100,164)
j_indices = slice(100,164)
z_indices = 100

image[i_indices, j_indices, z_indices]
1 Like
3

Thanks a lot, it worked