Problems during Skeletonization image for extracting contours

Question

I found this code to get a skeletonized image. I have a circle image
(https://docs.google.com/file/d/0ByS6Z5WRz-h2RXdzVGtXUTlPSGc/edit?usp=sharing).

img = cv2.imread(nomeimg,0)
size = np.size(img)
skel = np.zeros(img.shape,np.uint8)

ret,img = cv2.threshold(img,127,255,0)
element = cv2.getStructuringElement(cv2.MORPH_CROSS,(3,3))
done = False

while( not done):
    eroded = cv2.erode(img,element)
    temp = cv2.dilate(eroded,element)
    temp = cv2.subtract(img,temp)
    skel = cv2.bitwise_or(skel,temp)
    img = eroded.copy()

    zeros = size - cv2.countNonZero(img)
    if zeros==size:
        done = True

print("skel")
print(skel)

cv2.imshow("skel",skel)
cv2.waitKey(0)

The problem is that image result is not a “skeleton” but a set of points! My
purpose was to extract contour perimeter after i have skeletonized the image.
How can I edit my code to solve it? It is correct using cv2.findContours to
find skeleton circle?

Answer 1

You need to reverse white & black, and fill all the holes by call cv2.dilate
first:

import numpy as np
import cv2

img = cv2.imread("e_5.jpg",0)
size = np.size(img)
skel = np.zeros(img.shape,np.uint8)

ret,img = cv2.threshold(img,127,255,0)
element = cv2.getStructuringElement(cv2.MORPH_CROSS,(3,3))
img = 255 - img
img = cv2.dilate(img, element, iterations=3)

done = False

while( not done):
    eroded = cv2.erode(img,element)
    temp = cv2.dilate(eroded,element)
    temp = cv2.subtract(img,temp)
    skel = cv2.bitwise_or(skel,temp)
    img = eroded.copy()

    zeros = size - cv2.countNonZero(img)
    if zeros==size:
        done = True

Here is the result:

But, the result is not good, because there are many gaps. The following
algorithm is better, it uses functions in scipy.ndimage.morphology:

import scipy.ndimage.morphology as m
import numpy as np
import cv2

def skeletonize(img):
    h1 = np.array([[0, 0, 0],[0, 1, 0],[1, 1, 1]]) 
    m1 = np.array([[1, 1, 1],[0, 0, 0],[0, 0, 0]]) 
    h2 = np.array([[0, 0, 0],[1, 1, 0],[0, 1, 0]]) 
    m2 = np.array([[0, 1, 1],[0, 0, 1],[0, 0, 0]])    
    hit_list = [] 
    miss_list = []
    for k in range(4): 
        hit_list.append(np.rot90(h1, k))
        hit_list.append(np.rot90(h2, k))
        miss_list.append(np.rot90(m1, k))
        miss_list.append(np.rot90(m2, k))    
    img = img.copy()
    while True:
        last = img
        for hit, miss in zip(hit_list, miss_list): 
            hm = m.binary_hit_or_miss(img, hit, miss) 
            img = np.logical_and(img, np.logical_not(hm)) 
        if np.all(img == last):  
            break
    return img

img = cv2.imread("e_5.jpg",0)
ret,img = cv2.threshold(img,127,255,0)
element = cv2.getStructuringElement(cv2.MORPH_CROSS,(3,3))
img = 255 - img
img = cv2.dilate(img, element, iterations=3)

skel = skeletonize(img)
imshow(skel, cmap="gray", interpolation="nearest")

The result is: