How to fill a thresholding image (some white parts) opencv? - python

I<ve created a script to threshold a microscopic image and I would like to know how to fill some white spaces of the image. As you see in the picture my aim is to make a filter to separate only the blue zones. All other white zones (red arrow) should be erased or converted (filled out) to black.
Here is my code:
original = cv2.imread(inputfile + ".jpg")
#cv2.imread(inputfile + ".jpg")
original = cv2.resize(original, (1280, 960)) #resize of original image
img = cv2.cvtColor(original, cv2.COLOR_BGR2GRAY)
median = cv2.medianBlur(img, 3)
ret, th = cv2.threshold(median, 160, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
kernel = np.ones((1,1), np.uint8)
opening = cv2.morphologyEx(th, cv2.MORPH_OPEN, kernel)
edge_touching_removed = clear_border(opening)
contours, hierarchy = cv2.findContours(edge_touching_removed, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
The thing is ... after apply this threshold I will apply contours to the blue zone to caculate area. That is ok... but the thing is I don<t know how to erase the others zones.
Should I export that threshold image and I painted manually? I dont wanna do that... I was thinking that maybe there is a manual fill out code. I used the cv2 morphology but I dont know if I need to do another filter for that.
Thanks

Related

Compare two different images and find the differences

I have a webcam which takes pictures of a concrete slab. Now I want to check if there are objects on the slab or not. The objects could be anything and accordingly cannot be enumerated in a class. Unfortunately I cannot compare the webcam image directly with an image without objects on the concrete slab, because the image of the camera could shift minimally in x and y direction and the lighting is also not always the same. So I cannot use cv2.substract.
I would prefer a foreground and background substract, where the background is just my concrete slab and the foreground is then the objects. But since the objects don´t move but lie still on the slab, I can´t use cv2.createBackgroundSubtractorMOG2() either.
The Pictures look like this:
The Concrete slap without any objects:
The slap with Objects:
In Python/OpenCV, you could do division normalization to even out the illumination and make the background white. Then do your subtraction. Then use morphology to clean up small regions. Then find contours and discard any small regions that are due to noise left after the division normalization and morphology.
Here is how to do division normalization.
Input 1:
Input 2:
import cv2
import numpy as np
# load image
img1 = cv2.imread("img1.jpg")
img2 = cv2.imread("img2.jpg")
# convert to grayscale
gray1 = cv2.cvtColor(img1, cv2.COLOR_BGR2GRAY)
gray2 = cv2.cvtColor(img2, cv2.COLOR_BGR2GRAY)
# blur
blur1 = cv2.GaussianBlur(gray1, (0,0), sigmaX=13, sigmaY=13)
blur2 = cv2.GaussianBlur(gray2, (0,0), sigmaX=13, sigmaY=13)
# divide
divide1 = cv2.divide(gray1, blur1, scale=255)
divide2 = cv2.divide(gray2, blur2, scale=255)
# threshold
thresh1 = cv2.threshold(divide1, 200, 255, cv2.THRESH_BINARY)[1]
thresh2 = cv2.threshold(divide2, 200, 255, cv2.THRESH_BINARY)[1]
# morphology
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (3,3))
morph1 = cv2.morphologyEx(thresh1, cv2.MORPH_OPEN, kernel)
morph2 = cv2.morphologyEx(thresh2, cv2.MORPH_OPEN, kernel)
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (5,5))
morph1 = cv2.morphologyEx(morph1, cv2.MORPH_CLOSE, kernel)
morph2 = cv2.morphologyEx(morph2, cv2.MORPH_CLOSE, kernel)
# write result to disk
cv2.imwrite("img1_division_normalize.jpg", divide1)
cv2.imwrite("img2_division_normalize.jpg", divide2)
cv2.imwrite("img1_division_morph1.jpg", morph1)
cv2.imwrite("img1_division_morph2.jpg", morph2)
# display it
cv2.imshow("img1_norm", divide1)
cv2.imshow("img2_norm", divide2)
cv2.imshow("img1_thresh", thresh1)
cv2.imshow("img2_thresh", thresh2)
cv2.imshow("img1_morph", morph1)
cv2.imshow("img2_morph", morph2)
cv2.waitKey(0)
cv2.destroyAllWindows()
Image 1 Normalized:
Image 2 Normalized:
Image 1 thresholded and morphology cleaned:
Image 2 thresholded and morphology cleaned:
In this case, Image 1 becomes completely white. So it (and subtraction) is not really needed. You just need to find contours for the second image result and if necessary discard tiny regions by area. The rest are your objects.

Refine OpenCV mask edge

I'm in the process of scanning old photographs, and I would like to automate the process of extracting the photograph from the (noisy) solid white background of the scanner so that I have a transparent photograph. This part of the program now works, but I have one more small problem with this.
The photograph can now be accurately detected (and extracted), but it leaves a small and sharp black border from the background around the entire photograph. I've tried to apply a gaussian blur to the transparency mask, but this wouldn't smooth the blackness away (and it made the border of the photograph look 'smudged').
This is the code that I have to extract the photo and generate the transparency mask:
# Load the scan, and convert it to RGBA.
original = cv2.imread('input.jpg')
original = cv2.cvtColor(original, cv2.COLOR_BGR2BGRA)
# Make the scan grayscale, and apply a blur.
image = cv2.cvtColor(original, cv2.COLOR_BGR2GRAY)
image = cv2.GaussianBlur(image, (25, 25), 0)
# Binarize the scan.
retval, threshold = cv2.threshold(image, 50, 255, cv2.THRESH_BINARY)
# Find the contour of the object.
contours, hierarchy = cv2.findContours(threshold, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
largestContourArea = -1
largestContour = -1
for contour in contours:
area = cv2.contourArea(contour)
if area > largestContourArea:
largestContourArea = area
largestContour = contour
# Generate the transparency mask.
mask = numpy.zeros(original.shape, numpy.uint8)
cv2.drawContours(mask, [ largestContour ], -1, (255, 255, 255, 255), -1)
# Apply the transparency mask.
original = cv2.multiply(mask.astype(float) / 255.0, original.astype(float))
cv2.imwrite('output.png', original)
I have a sample scan and the result of the code above using the sample scan. As you can see, there is a slight black border all around the photograph, which I would like to remove.
By using the erode method, you could shrink the contour (mask), effectively removing the black edge.
Since this method supports in-place operation, the code would look something like this: cv2.erode(mask, mask, kernel), where kernel is a kernel acquired using cv2.getStructuringElement. By playing around with the kernel and the iteration count, you can control the amount of shrinking.
This page explains everything in great detail and also provides nice examples: https://docs.opencv.org/2.4/doc/tutorials/imgproc/erosion_dilatation/erosion_dilatation.html

find rectangle in image and extract text inside of it to save it as new image

I am new to OpenCV so I really need your help. I have a bunch of images like this one:
I need to detect the rectangle on the image, extract the text part from it and save it as a new image.
Can you please help me with this?
Thank you!
Just to add to Danyals answer I have added an example code with steps written in comments. For this image you don't even need to perform morphological opening on the image. But usually for this kind of noise in the image it is recomended. Cheers!
import cv2
import numpy as np
# Read the image and create a blank mask
img = cv2.imread('napis.jpg')
h,w = img.shape[:2]
mask = np.zeros((h,w), np.uint8)
# Transform to gray colorspace and invert Otsu threshold the image
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
_, thresh = cv2.threshold(gray,0,255,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)
# ***OPTIONAL FOR THIS IMAGE
### Perform opening (erosion followed by dilation)
#kernel = np.ones((2,2),np.uint8)
#opening = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
# ***
# Search for contours, select the biggest and draw it on the mask
_, contours, hierarchy = cv2.findContours(thresh, # if you use opening then change "thresh" to "opening"
cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
cnt = max(contours, key=cv2.contourArea)
cv2.drawContours(mask, [cnt], 0, 255, -1)
# Perform a bitwise operation
res = cv2.bitwise_and(img, img, mask=mask)
########### The result is a ROI with some noise
########### Clearing the noise
# Create a new mask
mask = np.zeros((h,w), np.uint8)
# Transform the resulting image to gray colorspace and Otsu threshold the image
gray = cv2.cvtColor(res,cv2.COLOR_BGR2GRAY)
_, thresh = cv2.threshold(gray,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
# Search for contours and select the biggest one again
_, contours, hierarchy = cv2.findContours(thresh,cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
cnt = max(contours, key=cv2.contourArea)
# Draw it on the new mask and perform a bitwise operation again
cv2.drawContours(mask, [cnt], 0, 255, -1)
res = cv2.bitwise_and(img, img, mask=mask)
# If you will use pytesseract it is wise to make an aditional white border
# so that the letters arent on the borders
x,y,w,h = cv2.boundingRect(cnt)
cv2.rectangle(res,(x,y),(x+w,y+h),(255,255,255),1)
# Crop the result
final_image = res[y:y+h+1, x:x+w+1]
# Display the result
cv2.imshow('img', final_image)
cv2.waitKey(0)
cv2.destroyAllWindows()
Result:
One way to do this (if the rectangle sizes are somewhat predictable) is:
Convert the image to black and white
Invert the image
Perform morphological opening on the image from (2) with a horizontal line / rectangle (I tried with 2x30).
Perform morphological opening on the image from (2) with a vertical line (I tried it with 15x2).
Add the images from (3) and (4). You should only have a white rectangle now. Now can remove all corresponding rows and columns in the original image that are entirely zero in this image.

Remove little edges from picture in python with Opencv

I am new to OpenCv. I am trying to create a white and black cartoonist picture of person through OpenCV in python. I am kind of successful, in creating black and white cartoon type picture of person. But the problem is, I want to remove black little dots from the output image. Please help me. I want to remove these black dots as pointed in picture.
Here is my code.
image = cv2.imread('input1.jpg')
img_gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
img_gray = cv2.medianBlur(img_gray, 5)
edges = cv2.Laplacian(img_gray, cv2.CV_8U, ksize=5)
ret,mask =cv2.threshold(edges,100,255,cv2.THRESH_BINARY_INV)
image2 = cv2.bitwise_and(image, image, mask=mask)
cv2.imshow("Mask", mask)
You need to apply a filter to your image using OpenCV to remove the black dots (which are called "noise"). There are many 2D convolutions you can apply to the image.
Median Filter
This filter will find the median value of every pixel and its surrounding pixels. It can gather as many pixels away from the centre as you like amplifying the effect.
Gaussian Blur
You can apply another type of blurring which should remove noise, maybe not entirely but it will surely reduce it's effect. If you're working on black and white, which it seems you are, then this might actually remove noise entirely.
Edit
Try applying a median filter again after you apply the threshold, that should remove noise much better than before since the values are binary:
image = cv2.imread('input1.jpg')
img_gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
img_gray = cv2.medianBlur(img_gray, 5)
edges = cv2.Laplacian(img_gray, cv2.CV_8U, ksize=5)
ret,mask =cv2.threshold(edges,100,255,cv2.THRESH_BINARY_INV)
image2 = cv2.bitwise_and(image, image, mask=mask)
image2 = cv2.medianBlur(image2, 3) # this
cv2.imshow("Mask", mask)
Hope this helps!
You could also try to find little countours and draw them out. Something like this:
img = cv2.imread('input1.jpg')
imgray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
ret,thresh = cv2.threshold(imgray,220,255,0)
_, contours, hierarchy = cv2.findContours(thresh,cv2.RETR_TREE,cv2.CHAIN_APPROX_SIMPLE)
number_contours = len(contours)
print(number_contours)
for i in range(0, number_contours):
lenght = cv2.contourArea(contours[i])
if float(1)<lenght<float(5000):
cv2.drawContours(img, contours[i], 0, (255,255,255), 7)
cv2.imshow("image", img)
cv2.imwrite("brez_pikic.jpg", img)

Get area within contours Opencv Python?

I have used an adaptive thresholding technique to create a picture like the one below:
The code I used was:
image = cv2.adaptiveThreshold(image, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C, cv2.THRESH_BINARY_INV, 45, 0)
Then, I use this code to get contours:
cnt = cv2.findContours(image, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[0]
My goal is to generate a mask using all the pixels within the outer contour, so I want to fill in all pixels within the object to be white. How can I do this?
I have tried the code below to create a mask, but the resulting mask seems no different then the image after applying adaptive threshold
mask = np.zeros(image.shape[:2], np.uint8)
cv2.drawContours(mask, cnt, -1, 255, -1)
What you have is almost correct. If you take a look at your thresholded image, the reason why it isn't working is because your shoe object has gaps in the image. Specifically, what you're after is that you expect that the shoe has its perimeter to be all connected. If this were to happen, then if you extract the most external contour (which is what your code is doing), you should only have one contour which represents the outer perimeter of the object. Once you fill in the contour, then your shoe should be completely solid.
Because the perimeter of your shoe is not complete and broken, this results in disconnected white regions. Should you use findContours to find all of the contours, it will only find the contours of each of the white shapes and not the most outer perimeter. As such, if you try and use findContours, it'll give you the same result as the original image, because you're simply finding the perimeter of each white region inside the image, then filling in these regions with findContours.
What you need to do is ensure that the image is completely closed. What I would recommend you do is use morphology to close all of the disconnected regions together, then run a findContours call on this new image. Specifically, perform a binary morphological closing. What this does is that it takes disconnected white regions that are close together and ensures that they're connected. Use a morphological closing, and perhaps use something like a 7 x 7 square structuring element to close the shoe. This structuring element you can think of as the minimum separation between white regions to consider them as being connected.
As such, do something like this:
import numpy as np
import cv2
image = cv2.imread('...') # Load your image in here
# Your code to threshold
image = cv2.adaptiveThreshold(image, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C, cv2.THRESH_BINARY_INV, 45, 0)
# Perform morphology
se = np.ones((7,7), dtype='uint8')
image_close = cv2.morphologyEx(image, cv2.MORPH_CLOSE, se)
# Your code now applied to the closed image
cnt = cv2.findContours(image_close, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)[0]
mask = np.zeros(image.shape[:2], np.uint8)
cv2.drawContours(mask, cnt, -1, 255, -1)
This code essentially takes your thresholded image, and applies morphological closing to this image. After, we find the external contours of this image, and fill them in with white. FWIW, I downloaded your thresholded image, and tried this on my own. This is what I get with your image:
A simple approach would be to close the holes in the foreground to form a single contour with cv2.morphologyEx() and cv2.MORPH_CLOSE
Now that the external contour is filled, we can find the outer contour with cv2.findContours() and use cv2.fillPoly() to fill in all pixels with white
import cv2
# Load in image, convert to grayscale, and threshold
image = cv2.imread('1.png')
gray = cv2.cvtColor(image,cv2.COLOR_BGR2GRAY)
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY + cv2.THRESH_OTSU)[1]
# Close contour
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (7,7))
close = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel, iterations=1)
# Find outer contour and fill with white
cnts = cv2.findContours(close, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cnts = cnts[0] if len(cnts) == 2 else cnts[1]
cv2.fillPoly(close, cnts, [255,255,255])
cv2.imshow('close', close)
cv2.waitKey()

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