Vessel segmentation in retina image - python

I am trying to trace the vessels in a retina image. Currently I am using cv2's threshold functions to make the vessels contrast more with the surrounding retina:
from matplotlib import pyplot as plt
import cv2
img = cv2.imread('misc images/eye.jpeg',0)
img = cv2.medianBlur(img,5)
ret,th1 = cv2.threshold(img,127,255,cv2.THRESH_BINARY)
th2 = cv2.adaptiveThreshold(img,255,cv2.ADAPTIVE_THRESH_MEAN_C,\
cv2.THRESH_BINARY,11,2)
th3 = cv2.adaptiveThreshold(img,255,cv2.ADAPTIVE_THRESH_GAUSSIAN_C,\
cv2.THRESH_BINARY,11,2)
titles = ['Original Image', 'Global Thresholding (v = 127)',
'Adaptive Mean Thresholding', 'Adaptive Gaussian Thresholding']
images = [img, th1, th2, th3]
for i in range(4):
plt.subplot(2,2,i+1),plt.imshow(images[i],'gray')
plt.title(titles[i])
plt.xticks([]),plt.yticks([])
plt.show()
And this is the result:
All 3 methods still have a lot of background noise from the rest of the retina. What can I do to improve the accuracy of vessel tracing?


Here is another way to threshold your image using division normalization followed by filtering on contour area.
Read the input
Convert to gray
Apply morphology dilate (or apply gaussianBlur)
Divide input by dilated result
Threshold
Invert so vessels are white on black background
Find all contours
Filter contours to discard ones that are too small
Draw remaining contours in white on black image as mask
Apply mask to threshold image as first result
Apply mask to input as second result
Save results
Input
import cv2
import numpy as np
# read the image
img = cv2.imread('retina_eye.jpg')
# convert to gray
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
# apply morphology
kernel = cv2.getStructuringElement(cv2.MORPH_RECT , (5,5))
morph = cv2.morphologyEx(gray, cv2.MORPH_DILATE, kernel)
# divide gray by morphology image
division = cv2.divide(gray, morph, scale=255)
# threshold
thresh = cv2.threshold(division, 0, 255, cv2.THRESH_OTSU )[1]
# invert
thresh = 255 - thresh
# find contours and discard contours with small areas
mask = np.zeros_like(thresh)
contours = cv2.findContours(thresh, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
area_thresh = 10000
for cntr in contours:
area = cv2.contourArea(cntr)
if area > area_thresh:
cv2.drawContours(mask, [cntr], -1, 255, 2)
# apply mask to thresh
result1 = cv2.bitwise_and(thresh, mask)
mask = cv2.merge([mask,mask,mask])
result2 = cv2.bitwise_and(img, mask)
# save results
cv2.imwrite('retina_eye_division.jpg',division)
cv2.imwrite('retina_eye_thresh.jpg',thresh)
cv2.imwrite('retina_eye_mask.jpg',mask)
cv2.imwrite('retina_eye_result1.jpg',result1)
cv2.imwrite('retina_eye_result2.jpg',result2)
# show results
cv2.imshow('morph', morph)
cv2.imshow('division', division)
cv2.imshow('thresh', thresh)
cv2.imshow('mask', mask)
cv2.imshow('result1', result1)
cv2.imshow('result2', result2)
cv2.waitKey(0)
cv2.destroyAllWindows()
Division image:
Threshold image:
Mask image:
Result 1:
Result 2:

Related

Detect thick black lines in image with OpenCV

I have the following image of a lego board with some bricks on it
Now I am trying to detect the thick black lines (connecting the white squares) with OpenCV. I have already experimented a lot with HoughLinesP, converted the image to gray or b/w before, applied blur, ...
Nonthing led to usable results.
# Read image
img = cv2.imread('image.jpg', cv2.IMREAD_GRAYSCALE)
# Resize Image
img = cv2.resize(img, (0,0), fx=0.25, fy=0.25)
# Initialize output
out = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
# Median blurring to get rid of the noise; invert image
img = cv2.medianBlur(img, 5)
# Adaptive Treshold
bw = cv2.adaptiveThreshold(img,255,cv2.ADAPTIVE_THRESH_GAUSSIAN_C,\
cv2.THRESH_BINARY,15,8)
# HoughLinesP
linesP = cv2.HoughLinesP(bw, 500, np.pi / 180, 50, None, 50, 10)
# Draw Lines
if linesP is not None:
for i in range(0, len(linesP)):
l = linesP[i][0]
cv2.line(out, (l[0], l[1]), (l[2], l[3]), (0,0,255), 3, cv2.LINE_AA)
The adaptive treshold lets you see edges quite well, but with HoughLinesP you don't get anything usable out of it
What am I doing wrong?
Thanks, both #fmw42 and #jeru-luke for your great solutions to this problem! I liked isolating / masking the green board, so I combined both:
import cv2
import numpy as np
img = cv2.imread("image.jpg")
scale_percent = 50 # percent of original size
width = int(img.shape[1] * scale_percent / 100)
height = int(img.shape[0] * scale_percent / 100)
dim = (width, height)
# resize image
img = cv2.resize(img, dim, interpolation = cv2.INTER_AREA)
lab = cv2.cvtColor(img, cv2.COLOR_BGR2LAB)
a_component = lab[:,:,1]
# binary threshold the a-channel
th = cv2.threshold(a_component,127,255,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)[1]
# numpy black
black = np.zeros((img.shape[0],img.shape[1]),np.uint8)
# function to obtain the largest contour in given image after filling it
def get_region(image):
contours, hierarchy = cv2.findContours(image, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
c = max(contours, key = cv2.contourArea)
mask = cv2.drawContours(black,[c],0,255, -1)
return mask
mask = get_region(th)
# turning the region outside the green block white
green_block = cv2.bitwise_and(img, img, mask = mask)
green_block[black==0]=(255,255,255)
# median blur
median = cv2.medianBlur(green_block, 5)
# threshold on black
lower = (0,0,0)
upper = (15,15,15)
thresh = cv2.inRange(median, lower, upper)
# apply morphology open and close
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (3,3))
morph = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (29,29))
morph = cv2.morphologyEx(morph, cv2.MORPH_CLOSE, kernel)
# filter contours on area
contours = cv2.findContours(morph, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
result = green_block.copy()
for c in contours:
area = cv2.contourArea(c)
if area > 1000:
cv2.drawContours(result, [c], -1, (0, 0, 255), 2)
# view result
cv2.imshow("result", result)
cv2.waitKey(0)
cv2.destroyAllWindows()

Here I am presenting a repeated segmentation approach using color.
This answer is based on the usage of LAB color space
1. Isolating the green lego block
img = cv2.imread(image_path)
lab = cv2.cvtColor(img, cv2.COLOR_BGR2LAB)
a_component = lab[:,:,1]
# binary threshold the a-channel
th = cv2.threshold(a_component,127,255,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)[1]
th
# function to obtain the largest contour in given image after filling it
def get_region(image):
contours, hierarchy = cv2.findContours(image, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
c = max(contours, key = cv2.contourArea)
black = np.zeros((image.shape[0], image.shape[1]), np.uint8)
mask = cv2.drawContours(black,[c],0,255, -1)
return mask
mask = get_region(th)
mask
# turning the region outside the green block white
green_block = cv2.bitwise_and(img, img, mask = mask)
green_block[black==0]=(255,255,255)
green_block
2. Segmenting the road
To get an approximate region of the road, I subtracted the mask and th.
cv2.subtract() performs arithmetic subtraction, where cv2 will take care of negative values.
road = cv2.subtract(mask,th)
# `road` contains some unwanted spots/contours which are removed using the function "get_region"
only_road = get_region(road)
only_road
Masking only the road segment with the original image gives
road_colored = cv2.bitwise_and(img, img, mask = only_road)
road_colored[only_road==0]=(255,255,255)
road_colored
From the above image only the black regions (road) are present, which is easy to segment:
# converting to grayscale and applying threshold
th2 = cv2.threshold(road_colored[:,:,1],127,255,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)[1]
# using portion of the code from fmw42's answer, to get contours above certain area
contours = cv2.findContours(th2, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
result = img.copy()
for c in contours:
area = cv2.contourArea(c)
if area > 1000:
cv2.drawContours(result, [c], -1, (0, 0, 255), 4)
result
Note:
To clean up the end result, you can apply morphological operations on th2 before drawing contours.

Here is one way to do that in Python/OpenCV.
Read the image
Apply median blur
Threshold on black color using cv2.inRange()
Apply morphology to clean it up
Get contours and filter on area
Draw contours on input
Save the result
Input:
import cv2
import numpy as np
# read image
img = cv2.imread('black_lines.jpg')
# median blur
median = cv2.medianBlur(img, 5)
# threshold on black
lower = (0,0,0)
upper = (15,15,15)
thresh = cv2.inRange(median, lower, upper)
# apply morphology open and close
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (3,3))
morph = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (29,29))
morph = cv2.morphologyEx(morph, cv2.MORPH_CLOSE, kernel)
# filter contours on area
contours = cv2.findContours(morph, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
result = img.copy()
for c in contours:
area = cv2.contourArea(c)
if area > 1000:
cv2.drawContours(result, [c], -1, (0, 0, 255), 2)
# save result
cv2.imwrite("black_lines_threshold.jpg", thresh)
cv2.imwrite("black_lines_morphology.jpg", morph)
cv2.imwrite("black_lines_result.jpg", result)
# view result
cv2.imshow("threshold", thresh)
cv2.imshow("morphology", morph)
cv2.imshow("result", result)
cv2.waitKey(0)
cv2.destroyAllWindows()
Threshold image:
Morphology image:
Result:

Detect squares (paintings) in images and draw contour around them using python

I'm trying to detect and draw a rectangular contour on every painting on for example this image:
I followed some guides and did the following:
Grayscale conversion
Applied median blur
Sharpen image
Applied adaptive Threshold
Applied Morphological Gradient
Find contours
Draw contours
And got the following result:
I know it's messy but is there a way to somehow detect and draw a contour around the paintings better?
Here is the code I used:
path = '<PATH TO THE PICTURE>'
#reading in and showing original image
image = cv2.imread(path)
image = cv2.resize(image,(880,600)) # resize was nessecary because of the large images
cv2.imshow("original", image)
cv2.waitKey(0)
cv2.destroyAllWindows()
# grayscale conversion
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
cv2.imshow("painting_gray", gray)
cv2.waitKey(0)
cv2.destroyAllWindows()
# we need to find a way to detect the edges better so we implement a couple of things
# A little help was found on stackoverflow: https://stackoverflow.com/questions/55169645/square-detection-in-image
median = cv2.medianBlur(gray,5)
cv2.imshow("painting_median_blur", median) #we use median blur to smooth the image
cv2.waitKey(0)
cv2.destroyAllWindows()
# now we sharpen the image with help of following URL: https://www.analyticsvidhya.com/blog/2021/08/sharpening-an-image-using-opencv-library-in-python/
kernel = np.array([[0, -1, 0],
[-1, 5,-1],
[0, -1, 0]])
image_sharp = cv2.filter2D(src=median, ddepth=-1, kernel=kernel)
cv2.imshow('painting_sharpend', image_sharp)
cv2.waitKey(0)
cv2.destroyAllWindows()
# now we apply adapptive thresholding
# thresholding: https://opencv24-python-tutorials.readthedocs.io/en/latest/py_tutorials/py_imgproc/py_thresholding/py_thresholding.html#adaptive-thresholding
thresh = cv2.adaptiveThreshold(src=image_sharp,maxValue=255,adaptiveMethod=cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
thresholdType=cv2.THRESH_BINARY,blockSize=61,C=20)
cv2.imshow('thresholded image', thresh)
cv2.waitKey(0)
cv2.destroyAllWindows()
# lets apply a morphological transformation
kernel = np.ones((7,7),np.uint8)
gradient = cv2.morphologyEx(thresh, cv2.MORPH_GRADIENT, kernel)
cv2.imshow('dilated image', gradient)
cv2.waitKey(0)
cv2.destroyAllWindows()
# # lets now find the contours of the image
# # find contours: https://docs.opencv.org/4.x/dd/d49/tutorial_py_contour_features.html
contours, hierarchy = cv2.findContours(gradient, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
print("contours: ", len(contours))
print("hierachy: ", len(hierarchy))
print(hierarchy)
cv2.drawContours(image, contours, -1, (0,255,0), 3)
cv2.imshow("contour image", image)
cv2.waitKey(0)
cv2.destroyAllWindows()
Tips, help or code is appreciated!

Here's a simple approach:
Obtain binary image. We load the image, grayscale, Gaussian blur, then Otsu's threshold to obtain a binary image.
Two pass dilation to merge contours. At this point, we have a binary image but individual separated contours. Since we can assume that a painting is a single large square contour, we can merge small individual adjacent contours together to form a single contour. To do this, we create a vertical and horizontal kernel using cv2.getStructuringElement then dilate to merge them together. Depending on the image, you may need to adjust the kernel sizes or number of dilation iterations.
Detect paintings. Now we find contours and filter using contour area using a minimum threshold area to filter out small contours. Finally we obtain the bounding rectangle coordinates and draw the rectangle with cv2.rectangle.
Code
import cv2
# Load image, grayscale, Gaussian blur, Otsu's threshold
image = cv2.imread('1.jpeg')
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
blur = cv2.GaussianBlur(gray, (13,13), 0)
thresh = cv2.threshold(blur, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)[1]
# Two pass dilate with horizontal and vertical kernel
horizontal_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (9,5))
dilate = cv2.dilate(thresh, horizontal_kernel, iterations=2)
vertical_kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (5,9))
dilate = cv2.dilate(dilate, vertical_kernel, iterations=2)
# Find contours, filter using contour threshold area, and draw rectangle
cnts = cv2.findContours(dilate, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cnts = cnts[0] if len(cnts) == 2 else cnts[1]
for c in cnts:
area = cv2.contourArea(c)
if area > 20000:
x,y,w,h = cv2.boundingRect(c)
cv2.rectangle(image, (x, y), (x + w, y + h), (36, 255, 12), 3)
cv2.imshow('thresh', thresh)
cv2.imshow('dilate', dilate)
cv2.imshow('image', image)
cv2.waitKey()

So here is the actual size of the portrait frame.
So here is small code.
#!/usr/bin/python 37
#OpenCV 4.3.0, Raspberry Pi 3/B/4B-w/4/8GB RAM, Buster,v10.
#Date: 3rd, June, 2020
import cv2
# Load the image
img = cv2.imread('portrait.jpeg')
# convert to grayscale
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
edged = cv2.Canny(img, 120,890)
# Apply adaptive threshold
thresh = cv2.adaptiveThreshold(edged, 255, 1, 1, 11, 2)
thresh_color = cv2.cvtColor(thresh, cv2.COLOR_GRAY2BGR)
# apply some dilation and erosion to join the gaps - change iteration to detect more or less area's
thresh = cv2.dilate(thresh,None,iterations = 50)
thresh = cv2.erode(thresh,None,iterations = 50)
# Find the contours
contours,hierarchy = cv2.findContours(thresh,
cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
# For each contour, find the bounding rectangle and draw it
for cnt in contours:
area = cv2.contourArea(cnt)
if area > 20000:
x,y,w,h = cv2.boundingRect(cnt)
cv2.rectangle(img,
(x,y),(x+w,y+h),
(0,255,0),
2)
cv2.imshow('img',img)
cv2.waitKey(0)
cv2.destroyAllWindows()
Here is output:

How to remove mammography tag artifacts

I have a mammography image dataset (mini DDSM). These images show letter artifacts indicating left or right mamma and other useless information for my ML model, so I want to curate this dataset before training the model.
In this paper, Preprocessing of Digital Mammogram Image Based on
Otsu’s Threshold, they use Otsu's binarization and opening on the mammography to clean the image (page 5 of 10):
Their results
So far, I have coded this:
im = io.imread('/content/drive/MyDrive/TFM/DDSMPNG/ALL2/0.jpg')
# thresholding
thresh = im > filters.threshold_otsu(im)
# opening with a disk structure
disk = morphology.disk(5)
opened = morphology.binary_opening(thresh,disk)
# plotting
plt.figure(figsize=(10, 10))
plt.subplot(131)
plt.imshow(im,cmap='gray')
plt.subplot(132)
plt.imshow(opened,cmap='gray')
plt.imsave('/content/drive/MyDrive/TFM/DDSMPNG/Blackened/0.jpg',opened)
And these are the plots:
Results
I have also tried with a higher disk shape to do the opening, it seems to remove more white of the small letter artifact, but also crops a bit the mammography:
disk = morphology.disk(45)
opened = morphology.binary_opening(thresh,disk)
The result:
Result with disk shape (45,45)
I guess I will have to create some kind of mask with the binarization and apply it to the original image, but I am new to image processing libraries and I'm not sure how to achieve the results
EDIT 1: I tried #fmw42 suggestion and I have some issues with it (I work on Google Colab, dont know If it has something to do...):
First, with the image used as example on your code, it doesn't seem to work propperly, don't know why, I copied your code and just modified the path to the image as well as some subplots to see the results:
# read image
img = cv2.imread('/content/drive/MyDrive/TFM/DDSMPNG/ALL2/0.jpg')
hh, ww = img.shape[:2]
# convert to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# apply otsu thresholding
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_OTSU )[1]
# apply morphology close to remove small regions
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5,5))
morph = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel)
# apply morphology open to separate breast from other regions
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5,5))
morph = cv2.morphologyEx(morph, cv2.MORPH_OPEN, kernel)
# get largest contour
contours = cv2.findContours(morph, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
big_contour = max(contours, key=cv2.contourArea)
# draw largest contour as white filled on black background as mask
mask = np.zeros((hh,ww), dtype=np.uint8)
cv2.drawContours(mask, [big_contour], 0, 255, cv2.FILLED)
# dilate mask
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (55,55))
mask = cv2.morphologyEx(mask, cv2.MORPH_DILATE, kernel)
# apply mask to image
result = cv2.bitwise_and(img, img, mask=mask)
# save results
cv2.imwrite('/content/drive/MyDrive/TFM/DDSMPNG/Blackened/0.jpg', result)
# show resultls
plt.figure(figsize=(10, 10))
plt.subplot(141)
plt.imshow(thresh,cmap='gray')
plt.subplot(142)
plt.imshow(morph,cmap='gray')
plt.subplot(143)
plt.imshow(mask,cmap='gray')
plt.subplot(144)
plt.imshow(result,cmap='gray')
Results:
Second, for the rest of the images, it seems to work well for most of them, but it crops a bit the breast surface:
In your result image, it seems to be much more smooth, how can I achieve that?
Thanks in advance!
EDIT 2: #fmw42 solution works fine, if someone has the same issue, you only need to play with the kernel sizes of the morphological filters until the image behaves like his results on the answer.
Thank you so much!

Here is one way to process your image in Python/OpenCV.
- Read the input
- Convert to grayscale
- Otsu threshold
- Morphology processing
- Get largest contour from external contours
- Draw all contours as white filled on a black background except the largest as a mask and invert mask
- Apply the mask to the input image
- Save the results
Input:
import cv2
import numpy as np
# read image
img = cv2.imread("mammogram.png")
hh, ww = img.shape[:2]
# convert to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# apply otsu thresholding
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_OTSU )[1]
# apply morphology close to remove small regions
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5,5))
morph = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel)
# apply morphology open to separate breast from other regions
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5,5))
morph = cv2.morphologyEx(morph, cv2.MORPH_OPEN, kernel)
# apply morphology dilate to compensate for otsu threshold not getting some areas
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (29,29))
morph = cv2.morphologyEx(morph, cv2.MORPH_DILATE, kernel)
# get largest contour
contours = cv2.findContours(morph, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
big_contour = max(contours, key=cv2.contourArea)
big_contour_area = cv2.contourArea(big_contour)
# draw all contours but the largest as white filled on black background as mask
mask = np.zeros((hh,ww), dtype=np.uint8)
for cntr in contours:
area = cv2.contourArea(cntr)
if area != big_contour_area:
cv2.drawContours(mask, [cntr], 0, 255, cv2.FILLED)
# invert mask
mask = 255 - mask
# apply mask to image
result = cv2.bitwise_and(img, img, mask=mask)
# save results
cv2.imwrite('mammogram_thresh.jpg', thresh)
cv2.imwrite('mammogram_morph.jpg', morph)
cv2.imwrite('mammogram_mask.jpg', mask)
cv2.imwrite('mammogram_result.jpg', result)
# show resultls
cv2.imshow('thresh', thresh)
cv2.imshow('morph', morph)
cv2.imshow('mask', mask)
cv2.imshow('result', result)
cv2.waitKey(0)
cv2.destroyAllWindows()
Thresholded Image:
Morphology Processed Image:
Mask Image From Contours:
Result Image:
Alternate
- Read the input
- Convert to grayscale
- Otsu threshold
- Morphology processing
- Get largest contour from external contours
- Draw largest as white filled on black background as a mask
- Dilate mask
- Apply the mask to the input image
- Save the results
Input:
import cv2
import numpy as np
# read image
img = cv2.imread("mammogram.png")
hh, ww = img.shape[:2]
# convert to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# apply otsu thresholding
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_OTSU )[1]
# apply morphology close to remove small regions
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5,5))
morph = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel)
# apply morphology open to separate breast from other regions
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5,5))
morph = cv2.morphologyEx(morph, cv2.MORPH_OPEN, kernel)
# get largest contour
contours = cv2.findContours(morph, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
big_contour = max(contours, key=cv2.contourArea)
# draw largest contour as white filled on black background as mask
mask = np.zeros((hh,ww), dtype=np.uint8)
cv2.drawContours(mask, [big_contour], 0, 255, cv2.FILLED)
# dilate mask
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (55,55))
mask = cv2.morphologyEx(mask, cv2.MORPH_DILATE, kernel)
# apply mask to image
result = cv2.bitwise_and(img, img, mask=mask)
# save results
cv2.imwrite('mammogram_thresh.jpg', thresh)
cv2.imwrite('mammogram_morph2.jpg', morph)
cv2.imwrite('mammogram_mask2.jpg', mask)
cv2.imwrite('mammogram_result2.jpg', result)
# show resultls
cv2.imshow('thresh', thresh)
cv2.imshow('morph', morph)
cv2.imshow('mask', mask)
cv2.imshow('result', result)
cv2.waitKey(0)
cv2.destroyAllWindows()
Threshold Image:
Morphology Processed Image:
Mask Image:
Result:
ADDITION
Here is the second method of processing applied to your larger JPG image. I noted that it was about 6x in width and height. So I increased the morphology kernels by about 6x from 5 to 31. I also trimmed the image borders 40 pixels all around and then added back a black border of the same amounts.
Input:
import cv2
import numpy as np
# read image
img = cv2.imread("mammogram.jpg")
hh, ww = img.shape[:2]
# convert to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# shave 40 pixels all around
gray = gray[40:hh-40, 40:ww-40]
# add 40 pixel black border all around
gray = cv2.copyMakeBorder(gray, 40,40,40,40, cv2.BORDER_CONSTANT, value=0)
# apply otsu thresholding
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_OTSU )[1]
# apply morphology close to remove small regions
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (31,31))
morph = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel)
# apply morphology open to separate breast from other regions
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (31,31))
morph = cv2.morphologyEx(morph, cv2.MORPH_OPEN, kernel)
# get largest contour
contours = cv2.findContours(morph, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
big_contour = max(contours, key=cv2.contourArea)
# draw largest contour as white filled on black background as mask
mask = np.zeros((hh,ww), dtype=np.uint8)
cv2.drawContours(mask, [big_contour], 0, 255, cv2.FILLED)
# dilate mask
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (305,305))
mask = cv2.morphologyEx(mask, cv2.MORPH_DILATE, kernel)
# apply mask to image
result = cv2.bitwise_and(img, img, mask=mask)
# save results
cv2.imwrite('mammogram_thresh.jpg', thresh)
cv2.imwrite('mammogram_morph2.jpg', morph)
cv2.imwrite('mammogram_mask2.jpg', mask)
cv2.imwrite('mammogram_result2.jpg', result)
# show resultls
cv2.imshow('thresh', thresh)
cv2.imshow('morph', morph)
cv2.imshow('mask', mask)
cv2.imshow('result', result)
cv2.waitKey(0)
cv2.destroyAllWindows()
Threshold Image:
Morphology Image:
Mask Image:
Result:

Crop exactly document paper from image

I am using the following code to crop image currently
def crop_image(image):
image = cv2.imread(image)
original_img = image.copy()
hsv_img = convert_hsv(image)
lower_blue = np.array([0, 0, 120])
upper_blue = np.array([180, 38, 255])
masked_image = mask_img(hsv_img, lower_blue, upper_blue)
result = cv2.bitwise_and(image, image, mask=masked_image)
contours = cv2.findContours(masked_image.copy(), cv2.RETR_LIST, cv2.CHAIN_APPROX_SIMPLE)
contours = imutils.grab_contours(contours)
cv2.drawContours(masked_image, contours, -1, (0, 255, 0), 3)
max_area_contour = max(contours, key=cv2.contourArea)
x, y, w, h = cv2.boundingRect(max_area_contour)
cv2.rectangle(result, (x, y), (x+w, y+h), (0, 255, 0), 3)
cont_filename = generate_contours_filename()
cv2.imwrite(cont_filename, np.hstack([image, result]))
logger.info('Successfuly saved file : %s' % cont_filename)
img = image[y:y+h, x:x+w]
filename = generate_filename()
cv2.imwrite(filename, img)
logger.info('Successfully saved cropped file : %s' % filename)
return img, filename
Following are theimages before and after:
This is original image
This is resulting image
I need image that crops paper part only
Thanks in advance

Here is one way to do that in Python/Opencv.
Read the input
Convert to grayscale
Threshold
Apply morphology to clean it of small regions
Get contours and filter to keep the largest one
Get the bounding box
Draw the largest contour filled on a black background as a mask
Apply the mask to blacken out the background of the paper
Use the bounding box to crop the masked input
Save the results
Input:
import cv2
import numpy as np
# read image as grayscale
img = cv2.imread('paper.jpg')
# convert to grayscale
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
# threshold
thresh = cv2.threshold(gray, 190, 255, cv2.THRESH_BINARY)[1]\
# apply morphology
kernel = np.ones((7,7), np.uint8)
morph = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel)
kernel = np.ones((9,9), np.uint8)
morph = cv2.morphologyEx(morph, cv2.MORPH_ERODE, kernel)
# get largest contour
contours = cv2.findContours(morph, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
contours = contours[0] if len(contours) == 2 else contours[1]
area_thresh = 0
for c in contours:
area = cv2.contourArea(c)
if area > area_thresh:
area_thresh = area
big_contour = c
# get bounding box
x,y,w,h = cv2.boundingRect(big_contour)
# draw filled contour on black background
mask = np.zeros_like(gray)
mask = cv2.merge([mask,mask,mask])
cv2.drawContours(mask, [big_contour], -1, (255,255,255), cv2.FILLED)
# apply mask to input
result1 = img.copy()
result1 = cv2.bitwise_and(result1, mask)
# crop result
result2 = result1[y:y+h, x:x+w]
# view result
cv2.imshow("threshold", thresh)
cv2.imshow("morph", morph)
cv2.imshow("mask", mask)
cv2.imshow("result1", result1)
cv2.imshow("result2", result2)
cv2.waitKey(0)
cv2.destroyAllWindows()
# save result
cv2.imwrite("paper_thresh.jpg", thresh)
cv2.imwrite("paper_morph.jpg", morph)
cv2.imwrite("paper_mask.jpg", mask)
cv2.imwrite("paper_result1.jpg", result1)
cv2.imwrite("paper_result2.jpg", result2)
Thresholded image:
Morphology cleaned image:
Mask image from largest contour:
Result of masking the input:
Result of cropping previous image:

Finding the corners of a rectangle

I'm trying to get the corners of this rectangle:
.
I tried using cv2.cornerHarris(rectangle, 2, 3, 0.04), but the left edges are not showed due to image brightness, I guess. So I tried applying a threshold before using cornerHarris, but the image produced showed a lot of vertices along the edges, not being possible to filter the corners.
I know that I need to filter it before using cornerHarris, but I don't know how. Could someone help me with this problem?
Ps. I've already tried to use blur, but it also doesn't work.
import cv2
import numpy as np
import matplotlib.pyplot as plt
rectangle = cv2.imread('rectangle.png', cv2.IMREAD_GRAYSCALE)
rectangle = np.where(rectangle > np.mean(rectangle), 255, 0).astype(np.uint8)
dst_rectangle = cv2.cornerHarris(rectangle, 2, 3, 0.04)
dst_rectangle = cv2.dilate(dst_rectangle, None)
mask = np.where(dst_rectangle > 0.01*np.max(dst_rectangle), 255, 0).astype(np.uint8)
points = np.nonzero(mask)
plt.imshow(dst_rectangle, cmap='gray')
plt.plot(points[1], points[0], 'or')
plt.show()

I would approach it differently by getting the corners of the rotated bounding box of the contour after adaptive thresholding. Here is my code in Python/OpenCV.
Input:
import cv2
import numpy as np
# read image
img = cv2.imread("rectangle.png")
# convert img to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
gray = 255-gray
# do adaptive threshold on gray image
thresh = cv2.adaptiveThreshold(gray, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY, 17, 1)
thresh = 255-thresh
# apply morphology
kernel = np.ones((3,3), np.uint8)
morph = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
morph = cv2.morphologyEx(morph, cv2.MORPH_CLOSE, kernel)
# separate horizontal and vertical lines to filter out spots outside the rectangle
kernel = np.ones((7,3), np.uint8)
vert = cv2.morphologyEx(morph, cv2.MORPH_OPEN, kernel)
kernel = np.ones((3,7), np.uint8)
horiz = cv2.morphologyEx(morph, cv2.MORPH_OPEN, kernel)
# combine
rect = cv2.add(horiz,vert)
# thin
kernel = np.ones((3,3), np.uint8)
rect = cv2.morphologyEx(rect, cv2.MORPH_ERODE, kernel)
# get largest contour
contours = cv2.findContours(rect, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
for c in contours:
area_thresh = 0
area = cv2.contourArea(c)
if area > area_thresh:
area = area_thresh
big_contour = c
# get rotated rectangle from contour
rot_rect = cv2.minAreaRect(big_contour)
box = cv2.boxPoints(rot_rect)
box = np.int0(box)
print(box)
# draw rotated rectangle on copy of img
rot_bbox = img.copy()
cv2.drawContours(rot_bbox,[box],0,(0,0,255),2)
# write img with red rotated bounding box to disk
cv2.imwrite("rectangle_thresh.png", thresh)
cv2.imwrite("rectangle_outline.png", rect)
cv2.imwrite("rectangle_bounds.png", rot_bbox)
# display it
cv2.imshow("IMAGE", img)
cv2.imshow("THRESHOLD", thresh)
cv2.imshow("MORPH", morph)
cv2.imshow("VERT", vert)
cv2.imshow("HORIZ", horiz)
cv2.imshow("RECT", rect)
cv2.imshow("BBOX", rot_bbox)
cv2.waitKey(0)
Thresholded Image:
Rectangle Region Extracted:
Rotated Bounding Box on Image:
Rotated Bounding Box Corners:
[[446 335]
[163 328]
[168 117]
[451 124]]
ADDITION:
Here is a slightly shorter version of the code, which is achievable by adding some gaussian blurring before thresholding.
import cv2
import numpy as np
# read image
img = cv2.imread("rectangle.png")
# convert img to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
gray = 255-gray
# blur image
blur = cv2.GaussianBlur(gray, (3,3), 0)
# do adaptive threshold on gray image
thresh = cv2.adaptiveThreshold(blur, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY, 75, 2)
thresh = 255-thresh
# apply morphology
kernel = np.ones((5,5), np.uint8)
rect = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
rect = cv2.morphologyEx(rect, cv2.MORPH_CLOSE, kernel)
# thin
kernel = np.ones((5,5), np.uint8)
rect = cv2.morphologyEx(rect, cv2.MORPH_ERODE, kernel)
# get largest contour
contours = cv2.findContours(rect, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
for c in contours:
area_thresh = 0
area = cv2.contourArea(c)
if area > area_thresh:
area = area_thresh
big_contour = c
# get rotated rectangle from contour
rot_rect = cv2.minAreaRect(big_contour)
box = cv2.boxPoints(rot_rect)
box = np.int0(box)
for p in box:
pt = (p[0],p[1])
print(pt)
# draw rotated rectangle on copy of img
rot_bbox = img.copy()
cv2.drawContours(rot_bbox,[box],0,(0,0,255),2)
# write img with red rotated bounding box to disk
cv2.imwrite("rectangle_thresh.png", thresh)
cv2.imwrite("rectangle_outline.png", rect)
cv2.imwrite("rectangle_bounds.png", rot_bbox)
# display it
cv2.imshow("IMAGE", img)
cv2.imshow("THRESHOLD", thresh)
cv2.imshow("RECT", rect)
cv2.imshow("BBOX", rot_bbox)
cv2.waitKey(0)
Thresholded Image:
Rectangle Region Extracted:
Rotated Bounding Box on Image:
Rotated Bounding Box Corners:
(444, 335)
(167, 330)
(170, 120)
(448, 125)

Here's a simple approach:
Obtain binary image. We load the image, grayscale, Gaussian blur, then adaptive threshold.
Morphological operations. We create a rectangular kernel and morph open to remove the small noise
Find distorted rectangle contour and draw onto a mask. Find contours, determine rotated bounding box, and draw onto a blank mask
Find corners. We use the Shi-Tomasi Corner Detector already implemented as cv2.goodFeaturesToTrack which is supposedly shows better results compared to the Harris Corner Detector
Here's a visualization of each step:
Binary image
Morph open
Find rotated rectangle contour and draw/fill onto a blank mask
Draw rotated rectangle and corners to get result
Corner coordinates
(448.0, 337.0)
(164.0, 332.0)
(452.0, 123.0)
(168.0, 118.0)
Code
import cv2
import numpy as np
# Load image, grayscale, Gaussian blur, adaptive threshold
image = cv2.imread("1.png")
mask = np.zeros(image.shape, dtype=np.uint8)
gray = 255 - cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
blur = cv2.GaussianBlur(gray, (3,3), 0)
thresh = cv2.adaptiveThreshold(blur, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY_INV, 51, 3)
# Morph open
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (3,3))
opening = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel, iterations=1)
# Find distorted rectangle contour and draw onto a mask
cnts = cv2.findContours(opening, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cnts = cnts[0] if len(cnts) == 2 else cnts[1]
rect = cv2.minAreaRect(cnts[0])
box = cv2.boxPoints(rect)
box = np.int0(box)
cv2.drawContours(image,[box],0,(36,255,12),2)
cv2.fillPoly(mask, [box], (255,255,255))
# Find corners on the mask
mask = cv2.cvtColor(mask, cv2.COLOR_BGR2GRAY)
corners = cv2.goodFeaturesToTrack(mask, maxCorners=4, qualityLevel=0.5, minDistance=150)
for corner in corners:
x,y = corner.ravel()
cv2.circle(image,(x,y),8,(255,120,255),-1)
print("({}, {})".format(x,y))
cv2.imshow("thresh", thresh)
cv2.imshow("opening", opening)
cv2.imshow("mask", mask)
cv2.imshow("image", image)
cv2.waitKey(0)

You can try with an adaptive threshold. Then you may either use cornerHarris if you only need corners, or depending on what you need to do next, you could also find useful findContours, which returns a list of bounding boxes

I was able to locate 3 out of the 4 points, the 4th point can be found easily given the other three points since it's rectangle. Here is my solution:
import cv2
import numpy as np
img = cv2.imread('6dUIr.png',1)
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
#smooth the image
kernel = np.ones((5,5),np.float32)/25
gray = cv2.filter2D(gray,-1,kernel)
#histogram equalization
clahe = cv2.createCLAHE(clipLimit=1.45, tileGridSize=(4,4))
cl1 = clahe.apply(gray)
#find edges
edges = cv2.Canny(cl1,4,100)
#find corners
dst = cv2.cornerHarris(edges,2,3,0.04)
#result is dilated for marking the corners, not important
dst = cv2.dilate(dst,None)
# Threshold for an optimal value, it may vary depending on the image.
img[dst>0.25*dst.max()]=[0,0,255]
cv2.imshow('edges', edges)
cv2.imshow('output', img)
# cv2.imshow('Histogram equalized', img_output)
cv2.waitKey(0)
The code has many hard coded thresholds but it's a good start.

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