Assignment to indexed images in SimpleITK

Question

What is the best way to do assign values or slices to indexed arrays in SimpleITK?

Example (1): Assigning a 2D slice to an indexed 2D slice in a 3D volume

In NumPy, we can do the following assignment to the index arrays:

import numpy as np
nda = np.ones((64, 256,256))
nda[0,:,:] = 2*nda[0,:,:]

The same operation in SimpleITK,

 import SimpleITK as sitk
 image = sitk.GetImageFromArray(nda)
 image[:,:,0] = 2*image[:,:,0]

gives the following error:

IndexError                                Traceback (most recent call last)
<ipython-input-18-4649e90a4ea5> in <module>
----> 1 image[:,:,0] = 2*image[:,:,0]

~/anaconda3/lib/python3.7/site-packages/SimpleITK/SimpleITK.py in __setitem__(self, idx, value)
 4690 
 4691     # the index parameter was an invalid set of objects
-> 4692         raise IndexError("invalid index")
 4693 
 4694 

IndexError: invalid index

Example (2): Assigning a value an indexed 2D slice in a 3D volume The following operation in NumPy,

  nda[0,:,:] = 2

n SimpleITK,

 image[:,:,0] = 2

gives the same Index error as in Example (1).

score 1 · Accepted Answer · answered Apr 22 '20 at 18:29

Unfortunately you can't do that type of operation in SimpleITK. The left hand side of the the assignment operator has to be a single pixel. It can't be a slice.

To do those types of operations, you'd have to extract out a slice from the volume, operate on the slice and then use the Paste function to paste the slice back into the volume.

You can see an example of the Paste function in an earlier answer I posted: https://stackoverflow.com/a/32612215/3712577

Assignment to indexed images in SimpleITK

1 Answers1