How to obtain boundary coordinates of binary mask with holes?

Question

I have the following image:

I would like to obtain a list with (x, y) -coordinates of the outer and inner contour for each blob (let's call them blob A and B).

import cv2
from skimage import measure

blob = cv2.imread('blob.png', 0)
contours, hier = cv2.findContours(blob, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
labels = measure.label(blob)
props = measure.regionprops(labels)

for ii in range(0,len(props))
xy = props[ii].coords

plt.figure(figsize=(18, 16))
plt.imshow(blob, cmap='gray')
plt.plot(xy[:, 0], xy[:,1])
plt.show()

Desired output image where blue and red are drawn from the (x, y) coordinate list A and B:

Answer 1

You get the (x, y) -coordinates directly from cv2.findContours . To identify the single blobs, have a look at the hierarchy hier . The fourth index tells you, to which outer (or parent) contour a possible inner (or child) contour is related. Most outer contours have an index of -1 , all other have non-negative values. So, for plotting/drawing, a naive approach would be, while iterating the contours, to increase a blob counter every time you see a -1 , and draw all contours with the same color until the next -1 shows.

import cv2
from skimage import io         # Only needed for web grabbing images, use cv2.imread for local images

# Read image; find contours with hierarchy
blob = io.imread('https://i.stack.imgur.com/Ga5Pe.png')
contours, hier = cv2.findContours(blob, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)

# Define sufficient enough colors for blobs
colors = [(255, 0, 0), (0, 255, 0), (0, 0, 255)]

# Draw all contours, and their children, with different colors
out = cv2.cvtColor(blob, cv2.COLOR_GRAY2BGR)
k = -1
for i, cnt in enumerate(contours):
    if (hier[0, i, 3] == -1):
        k += 1
    cv2.drawContours(out, [cnt], -1, colors[k], 2)

cv2.imshow('out', out)
cv2.waitKey(0)
cv2.destroyAllWindows()

Of course, obtaining all contours belonging to the same blob can be optimized using NumPy, but looping feels most intuitive here. I omitted all the other stuff (skimage, Matplotlib), since they didn't seem relevant here. As I said, the (x, y) -coordinates are already stored in contours .

Hope that helps!

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EDIT: I haven't validated, if OpenCV always obtains all contours belonging to one most outer contour continously, or if - for example - all contours for a given hierarchy level are stored subsequently. So, for more complicated hierarchies, this should be tested beforehand, or the mentioned index finding using NumPy should be used right from the start.