CODEWITHSUNDEEP
python-2.7image-processingscikit-image
KimHee
KimHee

Reputation: 788

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

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

enter image description here

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?

Upvotes: 5

Views: 19981

Answers (2)

Ningrong Ye
Ningrong Ye

Reputation: 1257

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

for example: enter image description here

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')

enter image description here

ref:scipy doc for binary fill holes

Upvotes: 0

user2999345
user2999345

Reputation: 4195

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

Upvotes: 6

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