Finding defects in the contours of a mask, derived from a complex medical image and correcting them

asked 2017-11-27 06:50:46 -0500

SLFWalsh gravatar image

updated 2020-04-08 06:35:25 -0500

I have several thousand images of the lungs, taken from a CT scanner. An image looks like this.

C:\fakepath\IM-0020-0085.jpg

I am attempting to extract the "lungs" section from the image by creating a mask. For example:

C:\fakepath\mask.jpg

The problem is the edges of the lungs in the mask. Ideally, I could perform contour approximation to approximate the boundaries of the lungs in the mask and smooth them out so that bits weren't chopped out.

To begin with, I have tried the following code - the idea being to find the contours and then the "defects". However in this code example, defects returns None. I am new to OpenCV:

     mask = cv2.imread("mask.jpg", 0)
     _, contours, hierarchy = cv2.findContours(mask, 1, 2)
     cnt = contours[0]
     hull = cv2.convexHull(cnt, returnPoints = False)
     defects = cv2.convexityDefects(cnt, hull)

    for i in range(defects.shape[0]):
          s,e,f,d = defects[i,0]
          start = tuple(cnt[s][0])
          end = tuple(cnt[e][0])
          far = tuple(cnt[f][0])
          cv2.line(img,start,end,[0,255,0],2)
          cv2.circle(img,far,5,[0,0,255],-1)

This work is a follow on from this question on stackoverflow

https://stackoverflow.com/questions/4...

Where it was suggested I look into contour approximation. I am wondering based on what I have researched so far, if it is contour hull I am really looking for. Any suggestions would be greatly appreciated.

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Comments

You're going to run into the same problem when using your own implementation of Marching Squares... I'm sorry, but what's wrong with the mask?

sjhalayka gravatar imagesjhalayka ( 2017-11-27 10:16:02 -0500 )edit

The edges of the mask cut out parts of the lung, because the bits of the lung on the original image at the edges are white (representing disease) - these white bits need to remain "within" the lung on the mask so that when I apply the mask to the lung image, those bits are preserved - they are important.

SLFWalsh gravatar imageSLFWalsh ( 2017-11-27 10:20:59 -0500 )edit

So basically, that particular lung slice is infested with diseased bits?

Anyway, your idea of grabbing the convex hull of the black region seems like a good solution.

You could also try running dilate() on the mask by like 10 pixels, and then erode() it by 10 pixels.

sjhalayka gravatar imagesjhalayka ( 2017-11-27 10:29:29 -0500 )edit

@SLFWalsh, the dilate() and erode() calls for Python are found here:

https://docs.opencv.org/3.0-beta/doc/...

By dilating and eroding, resulting mask can be found here: https://github.com/sjhalayka/random_i...

sjhalayka gravatar imagesjhalayka ( 2017-11-27 10:34:29 -0500 )edit

Can you provide this code in Python?

SLFWalsh gravatar imageSLFWalsh ( 2017-11-27 11:14:56 -0500 )edit

Sorry, I edited my last comment to remove the C++ code and put in a link to some Python code that dilates and erodes.

You can also try this code:

import cv2
import numpy as np

img = cv2.imread('input.png', 0)

kernel = np.ones((10, 10), np.uint8) # make a square dilation/erosion element

img = cv2.dilate(img, kernel, iterations=1)
img = cv2.erode(img, kernel, iterations=1)

cv2.imshow('Input', img)

cv2.waitKey(0)

Adjust the kernel size and iteration count to suit your needs. Also, look into getStructuringElement(), which provides circular or cross shaped (... not just square ...) dilation/erosion elements.

sjhalayka gravatar imagesjhalayka ( 2017-11-27 11:18:26 -0500 )edit

defects = cv2.convexityDefects(cnt, hull) is returning none value. Because of this I am not able to go further into defects.shape[0] where the error message is No shape attribute.

Could you please check this and let me know.

Sravan gravatar imageSravan ( 2018-02-05 08:23:33 -0500 )edit

@Sravan, please do not post answers here, if you have a question or comment, thank you.

berak gravatar imageberak ( 2018-02-05 09:13:20 -0500 )edit