How to completely fill holes to an image using the skimage?

Question

I am using skimage to fill holes a binary input image (left side). This is my code

from skimage import ndimage
img_fill_holes=ndimage.binary_fill_holes(binary).astype(int)

However, the result of the above code cannot completely fill holes to the binary image. It means the output still remains the holes inside the circle. How can I completely fill all holes inside the circle?

score 6 · Accepted Answer · answered May 13 '17 at 11:51

6

you were probably tried to apply binary_fill_holes on an RGB image (a 3D matrix, do binary.shape[2] == 3 to check that).

try:

img_fill_holes = ndimage.binary_fill_holes(binary[:,:,0]).astype(int)

or any other "rgb2gray" approach and you should get the expected output

answered May 13 '17 at 11:51

user2999345

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I have an array which is (301, 512,512) ,can i perform a similar operation on my array? – Ryan Apr 07 '18 at 10:31
2

I just tried this and there doesn't seem to be a `ndimage` subpackage in `skimage`. I tried importing `skimage.ndimage` and it said there was no such package. I did however find it in SciPy: https://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.ndimage.morphology.binary_fill_holes.html and the inputs and outputs are the same. – rayryeng Jul 03 '18 at 04:34
this will ony slice the first rows of the 3d array ,please explain how to process the whole 3d nparry – Hari Feb 24 '20 at 10:22

score 0 · Answer 2 · answered Nov 15 '21 at 04:59

if you have the 3D array, just change the structure to a 3d array.

for example:

import SimpleITK as sitk
from scipy import ndimage
brain_mask_raw = sitk.ReadImage('/PATH/TO/brain_mask.nii.gz')
brain_mask_array = sitk.GetArrayFromImage(brain_mask_raw)
brain_mask_array_filled = ndimage.binary_fill_holes(brain_mask_array, structure=np.ones((3,3,3))).astype(int)
brain_mask_filled = sitk.GetImageFromArray(brain_mask_array_filled.astype(brain_mask_array.dtype)).CopyInformation(brain_mask_raw)
sitk.WriteImage(brain_mask_filled, '/RESULT/PATH/brain_mask_filled.nii.gz')

ref:scipy doc for binary fill holes

How to completely fill holes to an image using the skimage?

2 Answers2