Is it possible to turn a 3D array to coordinate system?

Question

Is it possible to take a 3D array and and turn it into a coordinate system? My array consists of 0s and 1s. If the value is 1 I want to take the xyz coordinate. In the end I want to output all coordinates to a csv file.

import nibabel as nib

coord = []
img = nib.load('test.nii').get_fdata().astype(int)

test.nii array:

[[[0 0 0 ... 0 0 0]
  [0 0 0 ... 0 0 0]
  [0 0 1 ... 1 1 0]
  ...
  [0 0 0 ... 0 0 0]
  [0 0 0 ... 1 1 1]
  [0 1 0 ... 0 0 0]]

 [[1 0 0 ... 0 0 0]
  [0 0 1 ... 0 0 0]
  [0 1 0 ... 0 0 0]
  ...
  [0 1 0 ... 0 0 0]
  [0 1 0 ... 0 0 0]
  [0 0 0 ... 1 0 0]]

 [[0 0 0 ... 0 0 0]
  [0 0 0 ... 0 1 0]
  [0 0 0 ... 0 0 0]
  ...
  [0 0 0 ... 0 0 0]
  [0 0 0 ... 0 0 0]
  [0 1 0 ... 0 1 1]]

 ...

 [[0 0 0 ... 1 0 0]
  [0 0 1 ... 0 0 0]
  [0 0 1 ... 0 0 0]
  ...
  [0 0 0 ... 1 0 0]
  [0 0 0 ... 1 0 0]
  [0 0 0 ... 1 0 0]]

 [[0 0 0 ... 0 0 0]
  [0 0 0 ... 0 0 0]
  [0 0 0 ... 0 0 1]
  ...
  [0 1 0 ... 0 0 0]
  [1 0 0 ... 0 0 0]
  [1 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 1 0]
  [0 1 0 ... 0 0 0]]]

Could you please provide at least few lines of 'test.nii' content? — Marek Piotrowski, Aug 12 '20 at 20:05
does numpy.argwhere do the trick for you? https://numpy.org/doc/stable/reference/generated/numpy.argwhere.html — David Kaftan, Aug 13 '20 at 00:53

score 1 · Accepted Answer · answered Aug 13 '20 at 05:59

That might not necessarily be the best solution, but let's keep it simple (would be great if framework did that for us, but...well):

data = [[[0, 0, 0, 0, 0, 0],
         [0, 0, 0, 0, 0, 0],
         [0, 0, 1, 1, 1, 0],
         [0, 0, 0, 0, 0, 0],
         [0, 0, 0, 1, 1, 1],
         [0, 1, 0, 0, 0, 0]],
        [[1, 0, 0, 0, 0, 0],
         [0, 0, 1, 0, 0, 0],
         [0, 1, 0, 0, 0, 0],
         [0, 1, 0, 0, 0, 0],
         [0, 1, 0, 0, 0, 0],
         [0, 0, 0, 1, 0, 0]]]

for x in range(len(data)):
    for y in range(len(data[x])):
        for z in range(len(data[x][y])):
            if data[x][y][z] == 1:
                print(f"{x} {y} {z}")

yields:

score -1 · Answer 2 · answered Aug 13 '20 at 00:24

-1

Using np.where() you can get the row, col and depth index of elements that satisfy you condition. Try this:

row_idx, col_idx, depth_idx = np.where(img==1)

answered Aug 13 '20 at 00:24

endless_river

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3

Is it possible to turn a 3D array to coordinate system?

2 Answers2