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How to measure average thickness of labeled segmented image

I have an image and I've done some pre-processing on the that image. Below I showed my preprocessing:
img= cv2.imread("...my_drive...\\image_69.tif",0)
median=cv2.medianBlur(img,13)
ret, th = cv2.threshold(median, 0 , 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
kernel=np.ones((3,15),np.uint8)
closing1 = cv2.morphologyEx(th, cv2.MORPH_CLOSE, kernel, iterations=2)
kernel=np.ones((1,31),np.uint8)
closing2 = cv2.morphologyEx(closing1, cv2.MORPH_CLOSE, kernel)
kernel=np.ones((1,13),np.uint8)
opening1= cv2.morphologyEx(closing2, cv2.MORPH_OPEN, kernel, iterations=2)
So, basically I used "Threshold filtering" , "closing" and "opening" and the result looks like this:
Please note that when I used type(opening1), I got numpy.ndarray. So the image at this step is numpy array with 1021 x 1024 size.
Then I labeled my image:
label_image=measure.label(opening1, connectivity=opening1.ndim)
props= measure.regionprops_table (label_image, properties=['label', "area", "coords"])
and the result looks like this
Please note that when I used type(label_image), I got numpy.ndarray. So the image at this step is numpy array with 1021 x 1024 size.
As you can see, currently the image has 6 labels. Some of these labels are short and small pieces, so I tried to keep top 2 label based on area
slc=label_image
rps=regionprops(slc)
areas=[r.area for r in rps]
id=np.argsort(props["area"])[::-1]
new_slc=np.zeros_like(slc)
for i in id[:2]:
new_slc[tuple(rps[i].coords.T)]=i+1
Now the result looks like this:
It looks like I was successful in keeping 2 top regions (please note that by changing id[:2] you can select thickest white layer or thin layer). Now:
What I want to do: I want to find the average thickness of these two regions
Also, please note that I know each of my pixels is 314 nm
Can anyone here advise how I can do this task?
Original photo: Below I showed low quality of my original image, so you have better understanding as why I did all the pre-processing
you can also access the original photo here : https://www.mediafire.com/file/20h66aq83edy1h7/img.7z/file

Here is one way to do that in Python/OpenCV.
Read the input
Convert to gray
Threshold to binary
Get the contours and filter on area so that we have only the two primary lines
Sort by area
Select the first (smaller and thinner) contour
Draw it white filled on a black background
Get its skeleton
Get the points of the skeleton
Fit a line to the points and get the rotation angle of the skeleton
Loop over each of the two contours and draw them white filled on a black background. Then rotate to horizontal lines. Then get the vertical thickness of the lines from the average thickness along each column using np.count_nonzero() and print the value.
Save intermediate images
Input:
import cv2
import numpy as np
import skimage.morphology
import skimage.transform
import math
# read image
img = cv2.imread('lines.jpg')
# convert to grayscale
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
# threshold
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)[1]
# get contours
new_contours = []
img2 = np.zeros_like(thresh, dtype=np.uint8)
contour_img = thresh.copy()
contour_img = cv2.merge([contour_img,contour_img,contour_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 > 1000:
cv2.drawContours(contour_img, [cntr], 0, (0,0,255), 1)
cv2.drawContours(img2, [cntr], 0, (255), -1)
new_contours.append(cntr)
# sort contours by area
cnts_sort = sorted(new_contours, key=lambda x: cv2.contourArea(x), reverse=False)
# select first (smaller) sorted contour
first_contour = cnts_sort[0]
contour_first_img = np.zeros_like(thresh, dtype=np.uint8)
cv2.drawContours(contour_first_img, [first_contour], 0, (255), -1)
# thin smaller contour
thresh1 = (contour_first_img/255).astype(np.float64)
skeleton = skimage.morphology.skeletonize(thresh1)
skeleton = (255*skeleton).clip(0,255).astype(np.uint8)
# get skeleton points
pts = np.column_stack(np.where(skeleton.transpose()==255))
# fit line to pts
(vx,vy,x,y) = cv2.fitLine(pts, cv2.DIST_L2, 0, 0.01, 0.01)
#print(vx,vy,x,y)
x_axis = np.array([1, 0]) # unit vector in the same direction as the x axis
line_direction = np.array([vx, vy]) # unit vector in the same direction as your line
dot_product = np.dot(x_axis, line_direction)
[angle_line] = (180/math.pi)*np.arccos(dot_product)
print("angle:", angle_line)
# loop over each sorted contour
# draw contour filled on black background
# rotate
# get mean thickness from np.count_non-zeros
black = np.zeros_like(thresh, dtype=np.uint8)
i = 1
for cnt in cnts_sort:
cnt_img = black.copy()
cv2.drawContours(cnt_img, [cnt], 0, (255), -1)
cnt_img_rot = skimage.transform.rotate(cnt_img, angle_line, resize=False)
thickness = np.mean(np.count_nonzero(cnt_img_rot, axis=0))
print("line ",i,"=",thickness)
i = i + 1
# save resulting images
cv2.imwrite('lines_thresh.jpg',thresh)
cv2.imwrite('lines_filtered.jpg',img2)
cv2.imwrite('lines_small_contour_skeleton.jpg',skeleton )
# show thresh and result
cv2.imshow("thresh", thresh)
cv2.imshow("contours", contour_img)
cv2.imshow("lines_filtered", img2)
cv2.imshow("first_contour", contour_first_img)
cv2.imshow("skeleton", skeleton)
cv2.waitKey(0)
cv2.destroyAllWindows()
Threshold image:
Contour image:
Filtered contour image:
Skeleton image:
Angle (in degrees) and Thicknesses (in pixels):
angle: 3.1869032185349733
line 1 = 8.79219512195122
line 2 = 49.51609756097561
To get the thickness in nm, multiply thickness in pixels by your 314 nm/pixel.
ADDITION
If I start with your tiff image, the following shows my preprocessing, which is similar to yours.
import cv2
import numpy as np
import skimage.morphology
import skimage.transform
import math
# read image
img = cv2.imread('lines.tif')
# convert to grayscale
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
# threshold
thresh = cv2.threshold(gray, 128, 255, cv2.THRESH_BINARY)[1]
# apply morphology
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1,5))
morph = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (29,1))
morph = cv2.morphologyEx(morph, cv2.MORPH_CLOSE, kernel)
# get contours
new_contours = []
img2 = np.zeros_like(gray, dtype=np.uint8)
contour_img = gray.copy()
contour_img = cv2.merge([contour_img,contour_img,contour_img])
contours = cv2.findContours(morph , 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 > 1000:
cv2.drawContours(contour_img, [cntr], 0, (0,0,255), 1)
cv2.drawContours(img2, [cntr], 0, (255), -1)
new_contours.append(cntr)
# sort contours by area
cnts_sort = sorted(new_contours, key=lambda x: cv2.contourArea(x), reverse=False)
# select first (smaller) sorted contour
first_contour = cnts_sort[0]
contour_first_img = np.zeros_like(morph, dtype=np.uint8)
cv2.drawContours(contour_first_img, [first_contour], 0, (255), -1)
# thin smaller contour
thresh1 = (contour_first_img/255).astype(np.float64)
skeleton = skimage.morphology.skeletonize(thresh1)
skeleton = (255*skeleton).clip(0,255).astype(np.uint8)
# get skeleton points
pts = np.column_stack(np.where(skeleton.transpose()==255))
# fit line to pts
(vx,vy,x,y) = cv2.fitLine(pts, cv2.DIST_L2, 0, 0.01, 0.01)
#print(vx,vy,x,y)
x_axis = np.array([1, 0]) # unit vector in the same direction as the x axis
line_direction = np.array([vx, vy]) # unit vector in the same direction as your line
dot_product = np.dot(x_axis, line_direction)
[angle_line] = (180/math.pi)*np.arccos(dot_product)
print("angle:", angle_line)
# loop over each sorted contour
# draw contour filled on black background
# rotate
# get mean thickness from np.count_non-zeros
black = np.zeros_like(thresh, dtype=np.uint8)
i = 1
for cnt in cnts_sort:
cnt_img = black.copy()
cv2.drawContours(cnt_img, [cnt], 0, (255), -1)
cnt_img_rot = skimage.transform.rotate(cnt_img, angle_line, resize=False)
thickness = np.mean(np.count_nonzero(cnt_img_rot, axis=0))
print("line ",i,"=",thickness)
i = i + 1
# save resulting images
cv2.imwrite('lines_thresh2.jpg',thresh)
cv2.imwrite('lines_morph2.jpg',morph)
cv2.imwrite('lines_filtered2.jpg',img2)
cv2.imwrite('lines_small_contour_skeleton2.jpg',skeleton )
# show thresh and result
cv2.imshow("thresh", thresh)
cv2.imshow("morph", morph)
cv2.imshow("contours", contour_img)
cv2.imshow("lines_filtered", img2)
cv2.imshow("first_contour", contour_first_img)
cv2.imshow("skeleton", skeleton)
cv2.waitKey(0)
cv2.destroyAllWindows()
Threshold image:
Morphology image:
Filtered Lines image:
Skeleton image:
Angle (degrees) and Thickness (pixels):
angle: 3.206927978669998
line 1 = 9.26171875
line 2 = 49.693359375

Use Deskew to straighten up the image.
Then, count the pixels of each column of the color of the label you want to measure then divide it by the number of columns to get the average thickness

This can be done with various tools in scipy. Assume you have the image here:
I = PIL.Image.open("input.jpg")
img = np.array(I).mean(axis=2)
mask = img==255 # or some kind of thresholding
imshow(mask) #note this is a binary image, the green coloring is due to some kind of rendering artifact or aliasing
If one zooms in they can see split up regions
To get around that we can dilate the mask
from scipy import ndimage as ni
mask1 = ni.binary_dilation(mask, iterations=2)
imshow(mask1)
Now, we can find connected regions, and find the top regions with the most pixels, which should be the two lines of interest:
lab, nlab = ni.label(mask1)
max_labs = np.argsort([ (lab==i).sum() for i in range(1, nlab+1)])[::-1]+1
imshow(lab==max_labs[0])
and imshow(lab==max_labs[1])
Working with the first line as an example:
from scipy.stats import linregress
y0,x0 = np.where(lab==max_labs[0])
l0 = linregress( x0, y0)
xi,yi = np.arange(img.shape[3]), np.arange(img.shape[3])*l0.slope + l0.intercept
plot( xi, yi, 'r--')
Interpolate along this region at different y-intercepts and compute the average signal along each line
from scipy.interpolate import RectBivariateSpline
img0 = img.copy()
img0[~(lab==max_labs[0])] = 0 # set everything outside this line region to 0
rbv = RectBivariateSpline(np.arange(img.shape[0]), np.arange(img.shape[1]), img0)
prof0 = [rbv.ev(yi+i, xi).mean() for i in np.arange(-300,300)] # pick a wide window here (-300,300), can be more technical, but not necessary
plot(prof0)
Use your favorite method to compute the FWHM of this profile, then multiply by your pixel-to-nanometers factor.
I would just use a Gaussian fit to compute fwhm
xvals = np.arange(len(prof0))
yvals = np.array(prof0)
def func(p, xvals, yvals):
mu,var, amp = p
model = np.exp(-(xvals-mu)**2/2/var)*amp
resid = (model-yvals)**2
return resid.sum()
from scipy.optimize import minimize
x0 = 300,200,255 # initial estimate of mu, variance, amplitude
fit_gauss = minimize(func, x0=x0, args=(xvals, yvals), method='Nelder-Mead')
mu, var, amp = fit_gauss.x
fwhm = 2.355 * np.sqrt(var)
# display using matplotlib plot /hlines
plot( xvals, yvals)
plot( xvals, amp*np.exp(-(xvals-mu)**2/2/var) )
hlines(amp*0.5, mu-fwhm/2., mu+fwhm/2, color='r')
legend(("profile","fit gauss","fwhm=%.2f pix" % fwhm))
Finally, thickness=fwhm*314, or about 13 microns.
Following the exact same approach for the second line (lab==max_labs[1]) gives a thickness of about 2.2 microns:
Note, I was using interactive plotting to do this example, hence calls to imshow , plot etc. are meant motly as a reference to the reader. One may need to take extra steps to recreate the exact images I've uploaded (zooming etc).

Is there any way to crop an image inside a box?

I want to crop the image only inside the box or rectangle. I tried so many approaches but nothing worked.
import cv2
import numpy as np
img = cv2.imread("C:/Users/hp/Desktop/segmentation/add.jpeg", 0);
h, w = img.shape[:2]
# print(img.shape)
kernel = np.ones((3,3),np.uint8)
img2 = img.copy()
img2 = cv2.medianBlur(img2,5)
img2 = cv2.adaptiveThreshold(img2,255,cv2.ADAPTIVE_THRESH_GAUSSIAN_C,\
cv2.THRESH_BINARY,11,2)
img2 = 255 - img2
img2 = cv2.dilate(img2, kernel)
img2 = cv2.medianBlur(img2, 9)
img2 = cv2.medianBlur(img2, 9)
cv2.imshow('anything', img2)
cv2.waitKey(0)
cv2.destroyAllWindows()
position = np.where(img2 !=0)
x0 = position[0].min()
x1 = position[0].max()
y0 = position[1].min()
y1 = position[1].max()
print(x0,x1,y0,y1)
result = img[x0:x1,y0:y1]
cv2.imshow('anything', result)
cv2.waitKey(0)
cv2.destroyAllWindows()
Output should be the image inside the sqaure.

You can use contour detection for this. If your image has basically only a hand drawn rectangle in it, I think it's good enough to assume it's the largest closed contour in the image. From that contour, we can figure out a polygon/quadrilateral approximation and then finally get an approximate rectangle. I'll define some utilities at the beginning which I generally use to make my time easier when messing around with images:
def load_image(filename):
return cv2.imread(filename)
def bnw(image):
return cv2.cvtColor(image, cv2.COLOR_RGB2GRAY)
def col(image):
return cv2.cvtColor(image, cv2.COLOR_GRAY2RGB)
def fixrgb(image):
return cv2.cvtColor(image, cv2.COLOR_BGR2RGB)
def show_image(image, figsize=(7,7), cmap=None):
cmap = cmap if len(image.shape)==3 else 'gray'
plt.figure(figsize=figsize)
plt.imshow(image, cmap=cmap)
plt.show()
def AdaptiveThresh(gray):
blur = cv2.medianBlur(gray, 5)
adapt_type = cv2.ADAPTIVE_THRESH_GAUSSIAN_C
thresh_type = cv2.THRESH_BINARY_INV
return cv2.adaptiveThreshold(blur, 255, adapt_type, thresh_type, 11, 2)
def get_rect(pts):
xmin = pts[:,0,1].min()
ymin = pts[:,0,0].min()
xmax = pts[:,0,1].max()
ymax = pts[:,0,0].max()
return (ymin,xmin), (ymax,xmax)
Let's load the image and convert it to grayscale:
image_name = 'test.jpg'
image_original = fixrgb(load_image(image_name))
image_gray = 255-bnw(image_original)
show_image(image_gray)
Use some morph ops to enhance the image:
kernel = np.ones((3,3),np.uint8)
d = 255-cv2.dilate(image_gray,kernel,iterations = 1)
show_image(d)
Find the edges and enhance/denoise:
e = AdaptiveThresh(d)
show_image(e)
m = cv2.dilate(e,kernel,iterations = 1)
m = cv2.medianBlur(m,11)
m = cv2.dilate(m,kernel,iterations = 1)
show_image(m)
Contour detection:
contours, hierarchy = cv2.findContours(m, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
total_area = np.prod(image_gray.shape)
max_area = 0
for cnt in contours:
# Simplify contour
perimeter = cv2.arcLength(cnt, True)
approx = cv2.approxPolyDP(cnt, 0.03 * perimeter, True)
area = cv2.contourArea(approx)
# Shape is recrangular, so 4 points approximately and it's convex
if (len(approx) == 4 and cv2.isContourConvex(approx) and max_area<area<total_area):
max_area = cv2.contourArea(approx)
quad_polygon = approx
img1 = image_original.copy()
img2 = image_original.copy()
cv2.polylines(img1,[quad_polygon],True,(0,255,0),10)
show_image(img1)
tl, br = get_rect(quad_polygon)
cv2.rectangle(img2, tl, br, (0,255,0), 10)
show_image(img2)
So you can see the approximate polygon and the corresponding rectangle, using which you can get your crop. I suggest you play around with median blur and morphological ops like erosion, dilation, opening, closing etc and see which set of operations suits your images the best; I can't really say what's good from just one image. You can crop using the top left and bottom right coordinates:
show_image(image_original[tl[1]:br[1],tl[0]:br[0],:])

Draw the square with a different color (e.g red) so it can be distinguishable from other writing and background. Then threshold it so you get a black and white image: the red line will be white in this image. Get the coordinates of white pixels: from this set, select only the two pairs (minX, minY)(maxX,maxY). They are the top-left and bottom-right points of the box (remember that in an image the 0,0 point is on the top left of the image) and you can use them to crop the image.

Completing contour for "broken" image

I have a noisy gray-scale image for which I want to segment/mask the large arc spanning the image from the rest. I intend to mask the arc and all of the pixels above the arc.
To do this, I have thresholded the image to create a binary image, and used cv2.findContours() to trace the outline of the arc.
Original Image:
Image after Otsu threshold:
Threshold + Closing:
Contours of closed image:
As you can see, the closed image does not create a solid arc. Closing further causes the arc to lose it's shape. The green line is a contour of the closed image. The blue line is created with approxpolyDP() but I can't get it to work. Are there better ways to mask the arc in the image perhaps?
Here is my code:
import cv2, matplotlib
import numpy as np
import matplotlib.pyplot as plt
# read an image
img = cv2.imread('oct.png')
# get gray image and apply Gaussian blur
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
blur = cv2.GaussianBlur(gray, (5, 5), 0)
# get binary image
ret, thresh = cv2.threshold(blur, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)
# close image to "solidify" it
kernel = np.ones((3,3),np.uint8)
closing = cv2.morphologyEx(thresh,cv2.MORPH_CLOSE,kernel, iterations = 3)
# find contours
(_, contours, _) = cv2.findContours(closing, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cnt = contours[0]
max_area = cv2.contourArea(cnt)
for cont in contours:
if cv2.contourArea(cont) > max_area:
cnt = cont
max_area = cv2.contourArea(cont)
# define main arc contour approx. and hull
perimeter = cv2.arcLength(cnt, True)
epsilon = 0.1 * cv2.arcLength(cnt, True)
approx = cv2.approxPolyDP(cnt, epsilon, True)
# hull = cv2.convexHull(cnt)
# cv2.isContourConvex(cnt)
imgcopy = np.copy(img)
cv2.drawContours(imgcopy, [cnt], -1, (0, 255, 0), 3)
cv2.drawContours(imgcopy, [approx], -1, (0, 0, 255), 3)
# plot figures
plt.figure(1)
plt.imshow(imgcopy, cmap="gray")
plt.figure(2)
plt.imshow(thresh, cmap="gray")
plt.figure(3)
plt.imshow(closing, cmap="gray")

I would suggest to use a RANSAC method to fit 2 ellipses using edge information of the arc. Edge can be obtain simply by using canny or any other method you see fit. Of course this method can only work if the arc is elliptical. If its a straight line, you can replace the ellipse fitting part with a line fitting part.
Here is the result:
Here is the code:
import numpy as np
import cv2
import random as rp
def ransac_ellipse(iter, srcimg, x, y):
x_size = np.size(x)
best_count = x_size
for i in range(iter):
base = srcimg.copy()
# get 5 random points
r1 = int(rp.random() * x_size)
r2 = int(rp.random() * x_size)
r3 = int(rp.random() * x_size)
r4 = int(rp.random() * x_size)
r5 = int(rp.random() * x_size)
p1 = (x[r1],y[r1])
p2 = (x[r2],y[r2])
p3 = (x[r3],y[r3])
p4 = (x[r4],y[r4])
p5 = (x[r5],y[r5])
p_set = np.array((p1,p2,p3,p4,p5))
# fit ellipse
ellipse = cv2.fitEllipse(p_set)
# remove intersected ellipse
cv2.ellipse(base,ellipse,(0),1)
# count remain
local_count = cv2.countNonZero(base)
# if count is smaller than best, update
if local_count < best_count:
best_count = local_count
best_ellipse = ellipse
return best_ellipse
img = cv2.imread('arc.jpg',0)
# Speed up and remove noise
small = cv2.resize(img,(0,0),fx = 0.25,fy = 0.25)
# remove remaining noise
median = cv2.medianBlur(small,21)
# get canny edge
edge = cv2.Canny(median,180,20)
cv2.imshow("Edge",edge)
# obtain the non zero locations
y, x = np.where(edge > 0)
# ransac ellipse to get the outter circle
ellipse1 = ransac_ellipse(10000,edge,x,y)
# remove the outter circle
cv2.ellipse(edge,ellipse1,(0),2)
# ransac ellipse to get the inner circle
y, x = np.where(edge > 0)
ellipse2 = ransac_ellipse(10000,edge,x,y)
disp = cv2.cvtColor(small,cv2.COLOR_GRAY2BGR)
cv2.ellipse(disp,ellipse1,(0,0,255),1)
cv2.ellipse(disp,ellipse2,(0,0,255),1)
cv2.imshow("result",disp)
cv2.waitKey(0)

You are on the right path. Your closing will likely work better if you smooth the image a little bit first. I like to apply the thresholding at the end, after the morphological operations. In this case, it doesn't really matter which the order for closing and thresholding is, but keeping thresholding at the end helps later when refining the pre-processing. Once you threshold you loose a lot of information, you need to make sure you preserve all the information you will need, and thus filtering the image properly before thresholding is important.
Here is a quick attempt, I'm sure it can be refined:
import matplotlib.pyplot as pp
import PyDIP as dip
img = pp.imread('/Users/cris/Downloads/MipBB.jpg')
img = img[:,:,0]
smooth = dip.Gauss(img, [3]) # Gaussian smoothing with sigma=3
smooth = dip.Closing(smooth, 25) # Note! This uses a disk SE with diameter 25 pixels
out = dip.Threshold(smooth, 'triangle')[0]
pp.imsave('/Users/cris/Downloads/MipBB_out.png', out)
I used the triangle threshold method (also known as the chord method, or skewed bi-modality threshold, see P.L. Rosin, "Unimodal thresholding", Pattern Recognition 34(11):2083-2096, 2001) because it works better in this case.
The code uses PyDIP, but I'm sure you can re-create the same process using OpenCV.

OpenCV - using cv2.canny and cv2.findContours to find area with data on the heterogeneous images

This is my first question here so I'm asking for understanding. I have to process hundreds of the satellites images.
I try to find contour of the area of the useful data located on the image - only the largest one.
Then I want to save the coordinates of the few points (x,y) corresponding to this contour. In simplest case, the area is a square and can be represented by 4 points, but for more complicated shapes the contour will be approximated by a little more points (preferably no more than ~ fifteen). However I am still not be able to find the areas on my images. Sometimes the area touches the edge of the image. Therefore, in this script I enlarge the pictures and add additional boundaries filled by the background color. Examples of pictures you will find here satellite1,satellite2,satellite3
As you see the images can have different background colors and in addition they contain countries borders and legend. I have tried to use Aidenhjj tips OpenCV - using cv2.approxPolyDP() correctly and prepared my script. I tried many approaches, filtering and tune parameters but still can't succeed with my data. I am asking you for help.
import numpy as np
import cv2
import matplotlib.pyplot as plt
image = cv2.imread('image1.jpg')
image = cv2.resize(image, None,fx=0.25, fy=0.25, interpolation = cv2.INTER_CUBIC)
ysize, xsize, channels = image.shape
print("Image size: {} x {}".format(xsize, ysize))
#calculate the histograms in r,g,b channels, measure background color
r, g, b = cv2.split(image)
image_data = image
histr = cv2.calcHist([r],[0],None,[256],[0,256])
for y in range(0,len(histr)):
elem = histr[y]
if elem == histr.max():
break
else:
y = none
R=y
histr = cv2.calcHist([g],[0],None,[256],[0,256])
for y in range(0,len(histr)):
elem = histr[y]
if elem == histr.max():
break
else:
y = none
G=y
histr = cv2.calcHist([b],[0],None,[256],[0,256])
for y in range(0,len(histr)):
elem = histr[y]
if elem == histr.max():
break
else:
y = none
B=y
color = (R, G, B)
#add borders around the image colorized as background. This will allow me to find closed contour around area with data.
bordersize=100
new_xsize = xsize + bordersize*2
new_ysize = ysize + bordersize*2
#image_border.show()
image_border=cv2.copyMakeBorder(image, top=bordersize, bottom=bordersize, left=bordersize, right=bordersize, borderType= cv2.BORDER_CONSTANT, value=[R,G,B] )
#ysizeb, xsizeb, channelsb = image_border.shape
# get a blank canvas for drawing contour on and convert image to grayscale
canvas = np.zeros(image_border.shape, np.uint8)
#imgc = cv2.medianBlur(img,21)
img2gray = cv2.cvtColor(image_border,cv2.COLOR_BGR2GRAY)
# filter out country borders
kernel = np.ones((5,5),np.float32)/25
img2gray = cv2.filter2D(img2gray,-1,kernel)
# threshold the image and extract contours
thresh = cv2.adaptiveThreshold(img2gray,255,cv2.ADAPTIVE_THRESH_MEAN_C,cv2.THRESH_BINARY,11,11)
contours,hierarchy = cv2.findContours(thresh, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)
plt.subplot(111),plt.imshow(thresh,'gray')
plt.show()
# find the biggest area
cnt = contours[0]
max_area = cv2.contourArea(cnt)
for cont in contours:
if cv2.contourArea(cont) > max_area:
cnt = cont
max_area = cv2.contourArea(cont)
perimeter = cv2.arcLength(cnt,True)
epsilon = 0.01*cv2.arcLength(cnt,True)
approx = cv2.approxPolyDP(cnt,epsilon,True)
hull = cv2.convexHull(cnt)
# cv2.isContourConvex(cnt)
cv2.drawContours(canvas, cnt, -1, (0, 255, 0), 3)
cv2.drawContours(canvas, approx, -1, (0, 0, 255), 3)
#cv2.drawContours(canvas, [hull], -1, (0, 0, 255), 3)
cv2.imshow("Contour", canvas)
k = cv2.waitKey(0)
if k == 27: # wait for ESC key to exit
cv2.destroyAllWindows()

Python OpenCV curved image to square image

I have the following image:
I would like to remove the distortion using Python OpenCV. Is this possible.
I am trying to follow the tutorial at Sudoku Solver, but I get a blob with array dimensions 7,1,2 instead of 4,1,2; which I assume is due to the distortion in my image. My code so far is:
import cv2
import numpy as np
def rectify(h):
h = h.reshape((4,2))
hnew = np.zeros((4,2),dtype = np.float32)
add = h.sum(1)
hnew[0] = h[np.argmin(add)]
hnew[2] = h[np.argmax(add)]
diff = np.diff(h,axis = 1)
hnew[1] = h[np.argmin(diff)]
hnew[3] = h[np.argmax(diff)]
return hnew
img = cv2.imread('blokkies.jpg')
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# GaussianBlur(src, ksize, sigma1[, dst[, sigma2[, borderType]]]) -> dst
gray = cv2.GaussianBlur(gray, (5, 5), 0)
# adaptiveThreshold(src, maxValue, adaptiveMethod, thresholdType, blockSize, C[, dst]) -> dst
thresh = cv2.adaptiveThreshold(gray, 255, 1, 1, 11, 2)
contours, hierarchy = cv2.findContours(thresh, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
# Biggest blob is the square we are looking for. Results in 4x1x2 array.
# First row is the TOP-RIGHT corner. Second row is the TOP-LEFT corner. Third row is the BOTTOM-LEFT corner. Finally, fourth one is the BOTTOM-RIGHT corner.
# The problem is that, there is no guarantee that for next image, the corners found out will be in this same order.
# Change to uniform order with rectify. [TOP-LEFT, TOP-RIGHT, BOTTOM-RIGHT, BOTTOM-LEFT]
biggest = None
max_area = 0
for i in contours:
area = cv2.contourArea(i)
if area > 100:
peri = cv2.arcLength(i, True)
approx = cv2.approxPolyDP(i, 0.02 * peri, True)
if area > max_area and len(approx) == 4:
biggest = approx
max_area = area
print(approx.shape)
approx = rectify(approx)
h = np.array([ [0,0],[449,0],[449,449],[0,449] ],np.float32)
cv2.imshow('image', h)
cv2.waitKey(0)
cv2.destroyAllWindows()

Turns out the bug in the tutorial was to use:
approx = rectify(biggest)
Also there is this
Removing curve