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Python/OpenCV — Intelligent Centroid Tracking in Bacterial Images?

I'm currently working on an algorithm to detect bacterial centroids in microscopy images.
This question is a continuation of: OpenCV/Python — Matching Centroid Points of Bacteria in Two Images: Python/OpenCV — Matching Centroid Points of Bacteria in Two Images
I am using a modified version of the program proposed by Rahul Kedia.
https://stackoverflow.com/a/63049277/13696853
Currently, the issues in segmentation I am working on are:
Low Contrast
Clustering
The images below are sampled a second apart. However, in the latter image, one of the bacteria does not get detected.
Bright-field Image #1
Bright-Field Image #2
Bright-Field Contour Image #1
Bright-Field Contour Image #2
Bright-Field Image #1 (Unsegmented)
Bright-Field Image #2 (Unsegmented)
I want to know, given that I can successfully determine bacterial centroids in an image, can I use the data to intelligently look for the same bacteria in the subsequent image?
I haven't been able to find anything substantial online; I believe SIFT/SURF would likely be ineffective as the bacteria have the same appearance. Moreover, I am looking for specific points in the images. You can view my program below. Insert a specific path as indicated if you'd like to run the program.
import cv2
import numpy as np
import os
kernel = np.array([[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[1, 1, 1, 1, 1],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0]], dtype=np.uint8)
def e_d(image, it):
image = cv2.erode(image, kernel, iterations=it)
image = cv2.dilate(image, kernel, iterations=it)
return image
path = r"[INSERT PATH]"
img_files = [file for file in os.listdir(path)]
def segment_index(index: int):
segment_file(img_files[index])
def segment_file(img_file: str):
img_path = path + "\\" + img_file
print(img_path)
img = cv2.imread(img_path)
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# Applying adaptive mean thresholding
th = cv2.adaptiveThreshold(img, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY_INV, 11, 2)
# Removing small noise
th = e_d(th.copy(), 1)
# Finding contours with RETR_EXTERNAL flag and removing undesired contours and
# drawing them on a new image.
cnt, hie = cv2.findContours(th, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
cntImg = th.copy()
for contour in cnt:
x, y, w, h = cv2.boundingRect(contour)
# Eliminating the contour if its width is more than half of image width
# (bacteria will not be that big).
if w > img.shape[1] / 2:
continue
cntImg = cv2.drawContours(cntImg, [cv2.convexHull(contour)], -1, 255, -1)
# Removing almost all the remaining noise.
# (Some big circular noise will remain along with bacteria contours)
cntImg = e_d(cntImg, 3)
# Finding new filtered contours again
cnt2, hie2 = cv2.findContours(cntImg, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
# Now eliminating circular type noise contours by comparing each contour's
# extent of overlap with its enclosing circle.
finalContours = [] # This will contain the final bacteria contours
for contour in cnt2:
# Finding minimum enclosing circle
(x, y), radius = cv2.minEnclosingCircle(contour)
center = (int(x), int(y))
radius = int(radius)
# creating a image with only this circle drawn on it(filled with white colour)
circleImg = np.zeros(img.shape, dtype=np.uint8)
circleImg = cv2.circle(circleImg, center, radius, 255, -1)
# creating a image with only the contour drawn on it(filled with white colour)
contourImg = np.zeros(img.shape, dtype=np.uint8)
contourImg = cv2.drawContours(contourImg, [contour], -1, 255, -1)
# White pixels not common in both contour and circle will remain white
# else will become black.
union_inter = cv2.bitwise_xor(circleImg, contourImg)
# Finding ratio of the extent of overlap of contour to its enclosing circle.
# Smaller the ratio, more circular the contour.
ratio = np.sum(union_inter == 255) / np.sum(circleImg == 255)
# Storing only non circular contours(bacteria)
if ratio > 0.55:
finalContours.append(contour)
finalContours = np.asarray(finalContours)
# Finding center of bacteria and showing it.
bacteriaImg = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
for bacteria in finalContours:
M = cv2.moments(bacteria)
cx = int(M['m10'] / M['m00'])
cy = int(M['m01'] / M['m00'])
bacteriaImg = cv2.circle(bacteriaImg, (cx, cy), 5, (0, 0, 255), -1)
cv2.imshow("bacteriaImg", bacteriaImg)
cv2.waitKey(0)
# Segment Each Image
for i in range(len(img_files)):
segment_index(i)
Edit #1: Applying frmw42's approach, this image seems to get lost. I have tried adjusting a number of parameters but the image does not seem to show up.
Bright-Field Image #3
Bright-Field Image #4

Here is my Python/OpenCV code to extract your bacteria. I simply threshold, then get the contours and draw filled contours for those within a certain area range. I will let you do any further processing that you want. I simply viewed each step to make sure I have tuned the arguments appropriately before moving to the next step.
Input 1:
Input 2:
import cv2
import numpy as np
# read image
#img = cv2.imread("bacteria1.png")
img = cv2.imread("bacteria2.png")
# convert img to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
gray = 255 - gray
# do adaptive threshold on inverted gray image
thresh = cv2.adaptiveThreshold(gray, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY, 21, 5)
result = np.zeros_like(img)
contours = cv2.findContours(thresh , cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
for cntr in contours:
area = cv2.contourArea(cntr)
if area > 600 and area < 1100:
cv2.drawContours(result, [cntr], 0, (255,255,255), -1)
# write results to disk
#cv2.imwrite("bacteria_filled_contours1.png", result)
cv2.imwrite("bacteria_filled_contours2.png", result)
# display it
cv2.imshow("thresh", thresh)
cv2.imshow("result", result)
cv2.waitKey(0)
Result 1:
Result 2:
Adjust as desired.

It would seem that adaptive threshold is not able to handle all your various images. I suspect nothing simple will. You may need to use AI with training. Nevertheless, this works for your images: 1, 2 and 4 in Python/OpenCV. I make no guarantee that it will work for any of your other images.
First I found a simple threshold that seems to work, but brings in other regions. So since all your bacteria have similar shapes and range of orientations, I fit and ellipse to your bacteria and get the orientation of the major axis and filter the contours with area and angle.
import cv2
import numpy as np
# read image
#img = cv2.imread("bacteria1.png")
#img = cv2.imread("bacteria2.png")
img = cv2.imread("bacteria4.png")
# convert img to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
gray = 255 - gray
# median filter
#gray = cv2.medianBlur(gray, 1)
# do simple threshold on inverted gray image
thresh = cv2.threshold(gray, 170, 255, cv2.THRESH_BINARY)[1]
result = np.zeros_like(img)
contours = cv2.findContours(thresh , cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
for cntr in contours:
area = cv2.contourArea(cntr)
if area > 600 and area < 1100:
ellipse = cv2.fitEllipse(cntr)
(xc,yc),(d1,d2),angle = ellipse
if angle > 90:
angle = angle - 90
else:
angle = angle + 90
print(angle,area)
if angle >= 150 and angle <= 250:
cv2.drawContours(result, [cntr], 0, (255,255,255), -1)
# write results to disk
#cv2.imwrite("bacteria_filled_contours1.png", result)
#cv2.imwrite("bacteria_filled_contours2.png", result)
cv2.imwrite("bacteria_filled_contours4.png", result)
# display it
cv2.imshow("thresh", thresh)
cv2.imshow("result", result)
cv2.waitKey(0)
Result for image 1:
Result for image 2:
Result for image 4:
You might explore noise reduction before thresholding. I had some success with using some of ImageMagick tools and there is a Python version called Python Wand that uses ImageMagick.

Calculate the white pixel inside cv2.circle

I'm trying to implement identification of optic nerve glioma identification using python and openCV.
I need to do the following steps in order for me to classify optic nerve glioma successfully.
Find the brightest part of an image and put a circle on it using cv2.circle - Done
Calculate the white part on the image inside cv2.circle - Needs help
Here's my code for identifying the brightest part of the image
gray = cv2.GaussianBlur(gray, (371, 371), 0)
(minVal, maxVal, minLoc, maxLoc) = cv2.minMaxLoc(gray)
image = orig.copy()
cv2.circle(image, maxLoc, 371, (255, 0, 0), 2)
sought = [254,254,254]
amount = 0
for x in range(image.shape[0]):
for y in range(image.shape[1]):
b, g, r = image[x, y]
if (b, g, r) == sought:
amount += 1
print(amount)
image = imutils.resize(image, width=400)
# display the results of our newly improved method
cv2.imshow("Optic Image", image)
cv2.waitKey(0)
The code above returns the following output
What I'm trying to do now is to identify the size of the white region of the image inside the cv2.circle.
Thank you so much!

I am not sure what you consider as "white", but here is one way to do the counting in Python/OpenCV. Simply read the image. Convert to grayscale. Threshold it at some level. Then just count the number of white pixels in the thresholded image.
If I use your output image for my input (after removing your white border):
import cv2
import numpy as np
# read image
img = cv2.imread('optic.png')
# convert to HSV and extract saturation channel
gray = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
# threshold
thresh = cv2.threshold(gray, 175, 255, cv2.THRESH_BINARY)[1]
# count number of white pixels
count = np.sum(np.where(thresh == 255))
print("count =",count)
# write result to disk
cv2.imwrite("optic_thresh.png", thresh)
# display it
cv2.imshow("IMAGE", img)
cv2.imshow("THRESH", thresh)
cv2.waitKey(0)
Thresholded image:
Count of white pixels in threshold:
count = 1025729

I am still not sure what you consider as white and what you consider as the yellow circle. But here is another attempt using Python/OpenCV.
Read the input
Convert the input to the range 0 to 1 as 1D data
Use kmeans clustering to reduce the number of colors and convert back to range 0 to 255 as 2D image
Use inRange color thresholding to isolate the "yellow" area
Clean it up with morphology and get the contour
Get the minimum enclosing circle center and radius and bias the center a little
Draw an unfilled white circle on the input
Draw a white filled circle on a black background as a circle mask for the yellow area
Convert the input to grayscale
Threshold the grayscale image
Apply the mask to the thresholded grayscale image
Count the number of white pixels
Input:
import cv2
import numpy as np
from sklearn import cluster
# read image
img = cv2.imread('optic.png')
h, w, c = img.shape
# convert to range 0 to 1
image = img.copy()/255
# reshape to 1D array
image_1d = image.reshape(h*w, c)
# do kmeans processing
kmeans_cluster = cluster.KMeans(n_clusters=int(5))
kmeans_cluster.fit(image_1d)
cluster_centers = kmeans_cluster.cluster_centers_
cluster_labels = kmeans_cluster.labels_
# need to scale result back to range 0-255
newimage = cluster_centers[cluster_labels].reshape(h, w, c)*255.0
newimage = newimage.astype('uint8')
# threshold brightest region
lowcolor = (150,180,230)
highcolor = (170,200,250)
thresh1 = cv2.inRange(newimage, lowcolor, highcolor)
# apply morphology open and close
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (7,7))
thresh1 = cv2.morphologyEx(thresh1, cv2.MORPH_OPEN, kernel, iterations=1)
thresh1 = cv2.morphologyEx(thresh1, cv2.MORPH_CLOSE, kernel, iterations=1)
# get contour
cntrs = cv2.findContours(thresh1, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cntrs = cntrs[0] if len(cntrs) == 2 else cntrs[1]
c = cntrs[0]
# get enclosing circle and bias center, if desired, since it is slightly offset (or alternately, increase the radius)
bias = 5
center, radius = cv2.minEnclosingCircle(c)
cx = int(round(center[0]))-bias
cy = int(round(center[1]))+bias
rr = int(round(radius))
# draw filled circle over black and also outline circle over input
mask = np.zeros_like(img)
cv2.circle(mask, (cx,cy), rr, (255, 255, 255), -1)
circle = img.copy()
cv2.circle(circle, (cx,cy), rr, (255, 255, 255), 1)
# convert to gray
gray = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
# threshold gray image
thresh2 = cv2.threshold(gray, 200, 255, cv2.THRESH_BINARY)[1]
# apply mask to thresh2
thresh2 = cv2.bitwise_and(thresh2, mask[:,:,0])
# count number of white pixels
count = np.sum(np.where(thresh2 == 255))
print("count =",count)
# write result to disk
#cv2.imwrite("optic_thresh.png", thresh)
cv2.imwrite("optic_kmeans.png", newimage)
cv2.imwrite("optic_thresh1.png", thresh1)
cv2.imwrite("optic_mask.png", mask)
cv2.imwrite("optic_circle.png", circle)
cv2.imwrite("optic_thresh2.png", thresh2)
# display it
cv2.imshow("IMAGE", img)
cv2.imshow("KMEANS", newimage)
cv2.imshow("THRESH1", thresh1)
cv2.imshow("MASK", mask)
cv2.imshow("CIRCLE", circle)
cv2.imshow("GRAY", gray)
cv2.imshow("THRESH2", thresh2)
cv2.waitKey(0)
kmeans image:
inRange threshold image:
Circle on input:
Circle mask image:
Masked threshold image:
Count Results:
count = 443239

How to perform image segmentation of apples using Python OpenCV?

I have pictures of apple slices that have been soaked in an iodine solution. The goal is to segment the apples into individual regions of interest and evaluate the starch level of each one. This is for a school project so my goal is to test different methods of segmentation and objectively find the best solution whether it be a single technique or a combination of multiple techniques.
The problem is that so far I have only come close on one method. That method is using HoughCircles. I had originally planned to use the Watershed method, Morphological operations, or simple thresholding. This plan failed when I couldn't modify any of them to work.
The original images look similar to this, with varying shades of darkness of the apple
I've tried removing the background tray using cv2.inRange with HSV values, but it doesn't work well with darker apples.
This is what the HoughCircles produced on the original image with a grayscale and median blur applied, also with an attempted mask of the tray.
Any advice or direction on where to look next would be greatly appreciated. I can supply the code I'm using if that will help.
Thank you!
EDIT 1 : Adding some code and clarifying the question
Thank you for the responses. My real question is are there any other methods of segmentation that this scenario lends itself well to? I would like to try a couple different methods and compare results on a large set of photos. My next in line to try is using k-means segmentation. Also I'll add some code below to show what I've tried so far.
HSV COLOR FILTERING
import cv2
import numpy as np
# Load image
image = cv2.imread('ApplePic.jpg')
# Set minimum and max HSV values to display
lower = np.array([0, 0, 0])
upper = np.array([105, 200, 255])
# Create HSV Image and threshold into a range.
hsv = cv2.cvtColor(image, cv2.COLOR_BGR2HSV)
mask = cv2.inRange(hsv, lower, upper)
maskedImage = cv2.bitwise_and(image, image, mask=mask)
# Show Image
cv2.imshow('HSV Mask', image)
cv2.waitKey(0)
HoughCircles
# import the necessary packages
import numpy as np
import argparse
import cv2
import os
directory = os.fsencode('Photos\\Sample N 100')
for file in os.listdir(directory):
filename = os.fsdecode(file)
if filename.endswith('.jpg'):
# Load the image
image = cv2.imread('Photos\\Sample N 100\\' + filename)
# Calculate scale
scale_factor = 800 / image.shape[0]
width = int(image.shape[1] * scale_factor)
height = 800
dimension = (width, height)
min_radius = int((width / 10) * .8)
max_radius = int((width / 10) * 1.2)
# Resize image
image = cv2.resize(image, dimension, interpolation=cv2.INTER_AREA)
# Copy Image
output = image.copy()
# Grayscale Image
gray = cv2.medianBlur(cv2.cvtColor(image, cv2.COLOR_BGR2GRAY), 5)
# Detect circles in image
circles = cv2.HoughCircles(gray, cv2.HOUGH_GRADIENT, 1, min_radius * 2, 4, 60, 20, min_radius, max_radius)
# ensure at least some circles were found
if circles is not None:
# convert the (x, y) coordinates and radius of the circles to integers
circles = np.round(circles[0, :]).astype("int")
# loop over the (x, y) coordinates and radius of the circles
for (x, y, r) in circles:
# draw the circle in the output image, then draw a rectangle
# corresponding to the center of the circle
cv2.circle(output, (x, y), r, (0, 255, 0), 4)
cv2.rectangle(output, (x - 5, y - 5), (x + 5, y + 5), (0, 128, 255), -1)
cv2.putText(output, '(' + str(x) + ',' + str(y) + ',' + str(r) + ')', (x, y),
cv2.FONT_HERSHEY_COMPLEX_SMALL, 1, 255)
# show the output image
cv2.imshow("output", np.hstack([image, output, maskedImage]))
cv2.waitKey(0)
continue
else:
continue

An alternative approach to segmenting the apples is to perform Kmeans color segmentation before thresholding then using contour filtering to isolate the apple objects:
Apply Kmeans color segmentation. We load the image, resize smaller using imutils.resize then apply Kmeans color segmentation. Depending on the number of clusters, we can segment the image into the desired number of colors.
Obtain binary image. Next we convert to grayscale, Gaussian blur and Otsu's threshold.
Filter using contour approximation. We filter out non-circle contours and small noise.
Morphological operations. We perform a morph close to fill adjacent contours
Draw minimum enclosing circles using contour area as filter. We find contours and draw the approximated circles. For this we use two sections, one where there was a good threshold and another where we approximate the radius.
Kmeans color quantization with clusters=3 and binary image
Morph close and result
The "good" contours that had the radius automatically calculated using cv2.minEnclosingCircle is highlighted in green while the approximated contours are highlighted in teal. These approximated contours were not segmented well from the thresholding process so we average the "good" contours radius and use that to draw the circle.
Code
import cv2
import numpy as np
import imutils
# Kmeans color segmentation
def kmeans_color_quantization(image, clusters=8, rounds=1):
h, w = image.shape[:2]
samples = np.zeros([h*w,3], dtype=np.float32)
count = 0
for x in range(h):
for y in range(w):
samples[count] = image[x][y]
count += 1
compactness, labels, centers = cv2.kmeans(samples,
clusters,
None,
(cv2.TERM_CRITERIA_EPS + cv2.TERM_CRITERIA_MAX_ITER, 10000, 0.0001),
rounds,
cv2.KMEANS_RANDOM_CENTERS)
centers = np.uint8(centers)
res = centers[labels.flatten()]
return res.reshape((image.shape))
# Load image, resize smaller, perform kmeans, grayscale
# Apply Gaussian blur, Otsu's threshold
image = cv2.imread('1.jpg')
image = imutils.resize(image, width=600)
kmeans = kmeans_color_quantization(image, clusters=3)
gray = cv2.cvtColor(kmeans, cv2.COLOR_BGR2GRAY)
blur = cv2.GaussianBlur(gray, (9,9), 0)
thresh = cv2.threshold(blur, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)[1]
# Filter out contours not circle
cnts = cv2.findContours(thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cnts = cnts[0] if len(cnts) == 2 else cnts[1]
for c in cnts:
peri = cv2.arcLength(c, True)
approx = cv2.approxPolyDP(c, 0.04 * peri, True)
if len(approx) < 4:
cv2.drawContours(thresh, [c], -1, 0, -1)
# Morph close
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5,5))
close = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel, iterations=3)
# Find contours and draw minimum enclosing circles
# using contour area as filter
approximated_radius = 63
cnts = cv2.findContours(close, 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)
x,y,w,h = cv2.boundingRect(c)
# Large circles
if area > 6000 and area < 15000:
((x, y), r) = cv2.minEnclosingCircle(c)
cv2.circle(image, (int(x), int(y)), int(r), (36, 255, 12), 2)
# Small circles
elif area > 1000 and area < 6000:
((x, y), r) = cv2.minEnclosingCircle(c)
cv2.circle(image, (int(x), int(y)), approximated_radius, (200, 255, 12), 2)
cv2.imshow('kmeans', kmeans)
cv2.imshow('thresh', thresh)
cv2.imshow('close', close)
cv2.imshow('image', image)
cv2.waitKey()

Highlight all possible circles ( Bubble sheet choices ) in opencv

I am working on automatically correcting a bubble-sheet tests that are scanned.
Currently, I can extract the solutions part of the sheet and fix its rotation.
So I have this image.
The output image with detected contours
Running the following code yields in the output image
def get_answers(image):
display_normal("Just image",image)
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
blurry = cv2.GaussianBlur(gray, (3, 3), 1)
thresh = cv2.threshold(blurry, 225, 255,
cv2.THRESH_BINARY_INV)[1]
display_normal("Binary", thresh)
# find contours in the thresholded image, then initialize
# the list of contours that correspond to questions
cnts = cv2.findContours(thresh.copy(), cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_SIMPLE)
cnts = cnts[1]
questionCnts = []
# loop over the contours
for c in cnts:
# compute the bounding box of the contour, then use the
# bounding box to derive the aspect ratio
(x, y, w, h) = cv2.boundingRect(c)
ar = w / float(h)
# in order to label the contour as a question, region
# should be sufficiently wide, sufficiently tall, and
# have an aspect ratio approximately equal to 1
if w >= 18 and h >= 18 and 0.9 <= ar and ar <= 1.2:
questionCnts.append(c)
cv2.drawContours(image, questionCnts, -1, (255, 0, 0), 1)
display_normal("Image with contours",image.copy())
if(questionCnts < 45*4):
raise Exception("Didn't found all possible answers")
Here is the problem : I convert the input image to binary and try to find contours that looks like a circle, but I can't find the whole possible 45*4 choices.. I fail to detect some of these circles..
So is there any better idea/algorithm to do this specific task ?

You could have tried using adaptive threshold:
adapt_thresh = cv2.adaptiveThreshold(equ, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C, cv2.THRESH_BINARY_INV, 11, 2)
cv2.imshow('adapt_thresh.jpg', adapt_thresh)
(I resized the original image to keep it smaller)
UPDATE:
Another approach that I just performed.......
I equalized the gray scale image using histogram equalization:
equalized_img = cv2.equalizeHist(gray)
cv2.imshow('Equalized Image.jpg', equalized_img )
I then obtained the median of the equalized image using np.median(equalized_img) and applied a binary threshold by selecting all pixel values below [0.6 * median]
ret, thresh = cv2.threshold(equalized_img, lower, 255, 1)
cv2.imwrite("Final Image.jpg", thresh)
Now you can go ahead and find your desired contours on this image.
Hope it helps .. :)

Python OpenCV - Extrapolating the largest rectangle off of a set of contour points

I'm trying to make an OpenCV detect a bed in the image. I am running the usual Grayscale, Blur, Canny, and I've tried Convex Hull. However, since there's quite a number of "noise" which gives extra contours and messes up the object detection. Because of this, I am unable to detect the bed properly.
Here is the input image as well as the Canny Edge Detection result:
As you can see, it's almost there. I have the outline of the bed already, albeit, that the upper right corner has a gap - which is preventing me from detecting a closed rectangle.
Here's the code I'm running:
import cv2
import numpy as np
def contoursConvexHull(contours):
print("contours length = ", len(contours))
print("contours length of first item = ", len(contours[1]))
pts = []
for i in range(0, len(contours)):
for j in range(0, len(contours[i])):
pts.append(contours[i][j])
pts = np.array(pts)
result = cv2.convexHull(pts)
print(len(result))
return result
def auto_canny(image, sigma = 0.35):
# compute the mediam of the single channel pixel intensities
v = np.median(image)
# apply automatic Canny edge detection using the computed median
lower = int(max(0, (1.0 - sigma) * v))
upper = int(min(255, (1.0 + sigma) *v))
edged = cv2.Canny(image, lower, upper)
# return edged image
return edged
# Get our image in color mode (1)
src = cv2.imread("bed_cv.jpg", 1)
# Convert the color from BGR to Gray
srcGray = cv2.cvtColor(src, cv2.COLOR_BGR2GRAY)
# Use Gaussian Blur
srcBlur = cv2.GaussianBlur(srcGray, (3, 3), 0)
# ret is the returned value, otsu is an image
##ret, otsu = cv2.threshold(srcBlur, 0, 255,
## cv2.THRESH_BINARY+cv2.THRESH_OTSU)
# Use canny
##srcCanny = cv2.Canny(srcBlur, ret, ret*2, 3)
srcCanny1 = auto_canny(srcBlur, 0.70)
# im is the output image
# contours is the contour list
# I forgot what hierarchy was
im, contours, hierarchy = cv2.findContours(srcCanny1,
cv2.RETR_TREE,
cv2.CHAIN_APPROX_SIMPLE)
##cv2.drawContours(src, contours, -1, (0, 255, 0), 3)
ConvexHullPoints = contoursConvexHull(contours)
##cv2.polylines(src, [ConvexHullPoints], True, (0, 0, 255), 3)
cv2.imshow("Source", src)
cv2.imshow("Canny1", srcCanny1)
cv2.waitKey(0)
Since the contour of the bed isn't closed, I can't fit a rectangle nor detect the contour with the largest area.
The solution I can think of is to extrapolate the largest possible rectangle using the contour points in the hopes of bridging that small gap, but I'm not too sure how to proceed since the rectangle is incomplete.

Since you haven't provided any other examples, I provide an algorithm working with this case. But bare in mind that you will have to find ways of adapting it to however the light and background changes on other samples.
Since there is a lot of noise and a relatively high dynamic range, I suggest not to use Canny and instead use Adaptive Thresholding and Find Contours on that (it doesn't need edges as an input), that helps with choosing different threshold values for different parts of the image.
My result:
Code:
import cv2
import numpy as np
def clahe(img, clip_limit=2.0, grid_size=(8,8)):
clahe = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=grid_size)
return clahe.apply(img)
src = cv2.imread("bed.png")
# HSV thresholding to get rid of as much background as possible
hsv = cv2.cvtColor(src.copy(), cv2.COLOR_BGR2HSV)
lower_blue = np.array([0, 0, 120])
upper_blue = np.array([180, 38, 255])
mask = cv2.inRange(hsv, lower_blue, upper_blue)
result = cv2.bitwise_and(src, src, mask=mask)
b, g, r = cv2.split(result)
g = clahe(g, 5, (3, 3))
# Adaptive Thresholding to isolate the bed
img_blur = cv2.blur(g, (9, 9))
img_th = cv2.adaptiveThreshold(img_blur, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
cv2.THRESH_BINARY, 51, 2)
im, contours, hierarchy = cv2.findContours(img_th,
cv2.RETR_CCOMP,
cv2.CHAIN_APPROX_SIMPLE)
# Filter the rectangle by choosing only the big ones
# and choose the brightest rectangle as the bed
max_brightness = 0
canvas = src.copy()
for cnt in contours:
rect = cv2.boundingRect(cnt)
x, y, w, h = rect
if w*h > 40000:
mask = np.zeros(src.shape, np.uint8)
mask[y:y+h, x:x+w] = src[y:y+h, x:x+w]
brightness = np.sum(mask)
if brightness > max_brightness:
brightest_rectangle = rect
max_brightness = brightness
cv2.imshow("mask", mask)
cv2.waitKey(0)
x, y, w, h = brightest_rectangle
cv2.rectangle(canvas, (x, y), (x+w, y+h), (0, 255, 0), 1)
cv2.imshow("canvas", canvas)
cv2.imwrite("result.jpg", canvas)
cv2.waitKey(0)