sitk.GetArrayFromImage returns empty numpy array?

Question

I am working with 3D MR image data. In order to calculate the histogram, I converted from sitk.Image to an numpy arrray of dimension 3. While I am able to display each axial slice using matplotlib, the numpy array is completely empty in all three dimensions. Can someone explain what is going on?

import numpy as np
import SimpleITK as sitk
from myshow import myshow

img = sitk.ReadImage("mri.hdr")
nda = sitk.GetArrayFromImage(img)
myshow(img)
print nda

Output:

[[[ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  ..., 
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]]

 [[ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  ..., 
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]]

 [[ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  ..., 
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]]

 ..., 
 [[ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  ..., 
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]]

 [[ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  ..., 
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]]

 [[ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  ..., 
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]
  [ 0.  0.  0. ...,  0.  0.  0.]]]

NOTES:

myshow.py (https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/master/Python/myshow.py)
myshow.py visualizes a slice of img by using matplotlib
MR image data is in hdr/img (analyze) format.

Can you please post a sample of your code, so that we can follow your logic — DJK, Aug 09 '17 at 16:40
Edited! I'm fairly new to coding and stackoverflow. Please excuse me if I'm not presenting my question clearly. — DottedGlass, Aug 10 '17 at 15:39

score 1 · Accepted Answer · answered Aug 10 '17 at 16:44

You're fine. The data is there it's just that the print function is showing data from the beginning of the array (it's large). If you print the data for a specific pixel which has content you'll see a valid value:

print nda[200,56,87]

The indexes are assumed to be in the valid range.

sitk.GetArrayFromImage returns empty numpy array?

1 Answers1