'Image Processing - Skimage or other
I am new to image processing. I am trying out a few experiments.
- I have binarized my image with otsu
- Found connected pixels with skimage
from PIL import Image
import numpy as np
import skimage
im = Image.open("DMSO_Resized.png")
imgr = im.convert("L")
im2arr = np.array(imgr)
arr2im = Image.fromarray(im2arr)
thresh = skimage.filters.threshold_otsu(im2arr)
binary = im2arr > thresh
connected = skimage.morphology.label(binary)
I'd now like to count the number of background pixels that are either "completely" covered by other background pixels or "partially" covered.
For example, pixel[1][1] is partially covered
1 0 2
0 0 0
3 0 8
AND
For example, pixel[1][1] is completely covered
0 0 0
0 0 0
0 0 0
Is there a skimage or other package that has a method to do these ? Or would I have to implement them as an array processing loop ?
import numpy as np
from skimage import morphology
bad_connection = np.array([[1, 0, 0, 0, 1],
[1, 0, 0, 0, 1],
[1, 0, 0, 0, 1],
[1, 0, 1, 0, 1],
[1, 0, 0, 0, 1]], dtype=np.uint8)
expected_good = np.array([[0, 0, 1, 0, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0],
[0, 0, 0, 0, 0]], dtype=np.uint8)
another_bad = np.array([[1, 0, 0, 0, 1],
[1, 1, 0, 1, 1],
[1, 1, 1, 1, 1],
[1, 1, 0, 1, 1],
[1, 0, 0, 0, 1]], dtype=np.uint8)
another_good = np.array([[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]], dtype=np.uint8)
footprint = np.array([[1, 0, 0, 0, 1],
[1, 0, 0, 0, 1],
[1, 0, 0, 0, 1]], dtype=np.uint8)
Sources
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