I have the following retina image and I'm trying to draw a circle around the optic disk (the white round shape in retinal image). Here is the original image:
I applied adaptive thresholding then cv2.findcontour:
import cv2
def detectBlob(file):
# read image
img = cv2.imread(file)
imageName = file.split('.')[0]
# convert img to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# do adaptive threshold on gray image
thresh = cv2.adaptiveThreshold(gray, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY, 101, 3)
# apply morphology open then close
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (3,3))
blob = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (20,20))
blob = cv2.morphologyEx(blob, cv2.MORPH_CLOSE, kernel)
# invert blob
blob = (255 - blob)
# Get contours
cnts,hierarchy = cv2.findContours(blob, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
# write results to disk
result = img.copy()
cv2.drawContours(result, cnts, -1, (0, 0, 255), 3)
cv2.imwrite(imageName+"_threshold.jpg", thresh)
cv2.imwrite(imageName+"_blob.jpg", blob)
cv2.imwrite(imageName+"_contour.jpg", result)
detectBlob('16.png')
Here is the what the threshold looks like:
Here is the final output of contours:
Ideally I'm looking for such an output:
Adaptive thresholding fails because the filter size is much too small. And though we don't figure this out, the waves in the background are quite perturbating.
I obtained an interesting result by reducing the image resolution by a factor 16 and applying an adaptive filter of extent 99x99.
You need to identify larger structures. Ideally you need a structure size about 1/4 of the radius of the optic disk to balance results and processing time (experiment with larger sizes until acceptable).
Or you could downsample the image (reduce the resolution and make the picture smaller), which is more or less the same thing, even if you lose precision on the optic disk borders.
Related
I need help with OpenCV
I have a picture with a complex for lying on the ground now i need to extract this form from the picture and cleaned it from noise. But now there is a logo which i need to remove and 4 holes to identify.What i could do Original image
My code so far:
import cv2
import numpy as np
# Read the original image
img = cv2.imread('Amoebe_1.jpg')
# resize image
scale_down = 0.4
img = cv2.resize(img, None, fx= scale_down, fy= scale_down, interpolation= cv2.INTER_LINEAR)
# Display original image
cv2.imshow('Original', img)
cv2.waitKey(0)
# Denoising
dst = cv2.fastNlMeansDenoisingColored(img,None,20,10,10,21)
# Canny Edge Detection
edges = cv2.Canny(image=dst, threshold1=100, threshold2=200) # Canny Edge Detection
# Contour Detection
contours1, hierarchy1 = cv2.findContours(edges, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
# draw contours on the original image for `CHAIN_APPROX_SIMPLE`
image_copy1 = img.copy()
cv2.drawContours(image_copy1, contours1, -1, (0, 255, 0), 2, cv2.LINE_AA)
# see the results
cv2.imshow('Simple approximation', image_copy1)
# Display Canny Edge Detection Image
cv2.imshow('Canny Edge Detection', edges)
cv2.waitKey(0)
#Floodfill
h,w,chn = img.shape
seed = (w/2,h/2)
mask = np.zeros((h+2,w+2),np.uint8)
bucket = edges.copy()
cv2.floodFill(bucket, mask, (0,0), (255,255,255))
cv2.imshow('Mask', bucket)
cv2.waitKey(0)
cv2.destroyAllWindows()
Having a shot at this in ImageJ, extracting the red channel from the raw image gives me this:
Which is close to a binary image already. Running a small (3pix) median filter and thresholding gives this as a binary:
Running cv.findContours() on that last one and analysing contour areas should give you the little holes and the "eye". Use cv.drawContours() with the bigger objects to fill up the eye and logo area, maybe dilate() to fill small discrepancies.
I have some cropped images and I need images that have black texts on white background. Firstly I apply adaptive thresholding and then I try to remove noise. Although I tried a lot of noise removal techniques but when the image changed, the techniques I used failed.
The best method for converting image color to binary for my images is Adaptive Gaussian Thresholding. Here is my code:
im_gray = cv2.imread("image.jpg", cv2.IMREAD_GRAYSCALE)
image = cv2.GaussianBlur(im_gray, (5,5), 1)
th = cv2.adaptiveThreshold(image,255,cv2.ADAPTIVE_THRESH_GAUSSIAN_C,cv2.THRESH_BINARY,3,2)
I need smooth values, Decimal separator(dot) and postfix letters. How can I do this?
Before binarization, it is necessary to correct the nonuniform illumination of the background. For example, like this:
import cv2
image = cv2.imread('9qBsB.jpg')
image=cv2.cvtColor(image,cv2.COLOR_BGR2GRAY)
se=cv2.getStructuringElement(cv2.MORPH_RECT , (8,8))
bg=cv2.morphologyEx(image, cv2.MORPH_DILATE, se)
out_gray=cv2.divide(image, bg, scale=255)
out_binary=cv2.threshold(out_gray, 0, 255, cv2.THRESH_OTSU )[1]
cv2.imshow('binary', out_binary)
cv2.imwrite('binary.png',out_binary)
cv2.imshow('gray', out_gray)
cv2.imwrite('gray.png',out_gray)
Result:
You can do slightly better using division normalization in Python/OpenCV.
Input:
import cv2
import numpy as np
# load image
img = cv2.imread("license_plate.jpg")
# convert to grayscale
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# blur
blur = cv2.GaussianBlur(gray, (0,0), sigmaX=33, sigmaY=33)
# divide
divide = cv2.divide(gray, blur, scale=255)
# otsu threshold
thresh = cv2.threshold(divide, 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)[1]
# apply morphology
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (3,3))
morph = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel)
# write result to disk
cv2.imwrite("hebrew_text_division.jpg", divide)
cv2.imwrite("hebrew_text_division_threshold.jpg", thresh)
cv2.imwrite("hebrew_text_division_morph.jpg", morph)
# display it
cv2.imshow("gray", gray)
cv2.imshow("divide", divide)
cv2.imshow("thresh", thresh)
cv2.imshow("morph", morph)
cv2.waitKey(0)
cv2.destroyAllWindows()
Division Image:
Thresholded Image:
Morphology Cleaned Image:
Im assuming that you are preprocessing the image for OCR(Optical Character Recognition)
I had a project to detect license plates and these were the steps I did, you can apply them to your project. After greying the image try applying equalize histogram to the image, this allows the area's in the image with lower contrast to gain a higher contrast. Then blur the image to reduce the noise in the background. Next apply edge detection on the image, make sure that noise is sufficiently removed as ED is susceptible to it. Lastly, apply closing(dilation then erosion) on the image to close all the small holes inside the words.
Instead of erode and dilate, you can check this, that is basically both in one.
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (1,2))
morphology_img = cv2.morphologyEx(img_grey, cv2.MORPH_OPEN, kernel,iterations=1)
plt.imshow(morphology_img,'Greys_r')
MORPHOLOGICAL_TRANSFORMATIONS
I am working with videos, that have borders (margins) around them. Some have it along all 4 sides, some along left&right only and some along top&bottom only. Length of these margins is also not fixed.
I am extracting frames from these videos, as for example,
and
Both of these contain borders on the top and bottom.
Can anyone please suggest some methods to remove these borders from these images (in Python, preferably).
I came across some methods, like this on Stackoverflow, but this deals with an ideal situation where borders are perfectly black (0,0,0). But in my case, they may not be pitch black, and also may contain jittery noises too.
Any help/suggestions would be highly appreciated.
Here is one way to do that in Python/OpenCV.
Read the image
Convert to grayscale and invert
Threshold
Apply morphology to remove small black or white regions then invert again
Get the contour of the one region
Get the bounding box of that contour
Use numpy slicing to crop that area of the image to form the resulting image
Save the resulting image
import cv2
import numpy as np
# read image
img = cv2.imread('gymnast.png')
# convert to grayscale
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
# invert gray image
gray = 255 - gray
# gaussian blur
blur = cv2.GaussianBlur(gray, (3,3), 0)
# threshold
thresh = cv2.threshold(blur,236,255,cv2.THRESH_BINARY)[1]
# apply close and open morphology to fill tiny black and white holes
kernel = np.ones((5,5), np.uint8)
thresh = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel)
thresh = cv2.morphologyEx(thresh, cv2.MORPH_OPEN, kernel)
# invert thresh
thresh = 255 -thresh
# get contours (presumably just one around the nonzero pixels)
# then crop it to bounding rectangle
contours = cv2.findContours(thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
contours = contours[0] if len(contours) == 2 else contours[1]
cntr = contours[0]
x,y,w,h = cv2.boundingRect(cntr)
crop = img[y:y+h, x:x+w]
cv2.imshow("IMAGE", img)
cv2.imshow("THRESH", thresh)
cv2.imshow("CROP", crop)
cv2.waitKey(0)
cv2.destroyAllWindows()
# save cropped image
cv2.imwrite('gymnast_crop.png',crop)
cv2.imwrite('gymnast_crop.png',crop)
Input:
Thresholded and cleaned image:
Cropped Result:
I'm using pytesseract to convert images into text, however the accuracy isn't 100% since the images pixelate on resizing. Applying gaussian blur would smoothen the edges but blur the image making it impossible for OCR to detect text.
What sort of filter would smoothen the edges without blurring the image too much. The image looks something like this
Image
You can median blur image then try a series of morphological transformations, specifically cv2.MORPH_CLOSE with a 3x3 kernel seems to work well here. You can play with the kernel size and number of iterations to get desired results
import cv2
image = cv2.imread('1.png')
blur = cv2.medianBlur(image, 7)
gray = cv2.cvtColor(blur, cv2.COLOR_BGR2GRAY)
thresh = cv2.threshold(gray,125, 255,cv2.THRESH_BINARY_INV)[1]
kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (3,3))
close = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel, iterations=2)
result = 255 - close
cv2.imshow('thresh', thresh)
cv2.imshow('close', close)
cv2.imshow('result', result)
cv2.imwrite('result.png', result)
cv2.waitKey()
I am working with skin images, in recognition of skin blemishes, and due to the presence of noises, mainly by the presence of hairs, this work becomes more complicated.
I have an image example in which I work in an attempt to highlight only the skin spot, but due to the large number of hairs, the algorithm is not effective. With this, I would like you to help me develop an algorithm to remove or reduce the amount of hair so that I can only highlight my area of interest (ROI), which are the spots.
Algorithm used to highlight skin blemishes:
import numpy as np
import cv2
#Read the image and perform threshold
img = cv2.imread('IMD006.bmp')
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
blur = cv2.medianBlur(gray,5)
_,thresh = cv2.threshold(blur,0,255,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)
#Search for contours and select the biggest one
contours, hierarchy = cv2.findContours(thresh,cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
cnt = max(contours, key=cv2.contourArea)
#Create a new mask for the result image
h, w = img.shape[:2]
mask = np.zeros((h, w), np.uint8)
#Draw the contour on the new mask and perform the bitwise operation
cv2.drawContours(mask, [cnt],-1, 255, -1)
res = cv2.bitwise_and(img, img, mask=mask)
#Display the result
cv2.imwrite('IMD006.png', res)
#cv2.imshow('img', res)
cv2.waitKey(0)
cv2.destroyAllWindows()
Example image used:
How to deal with these noises to the point of improving my region of interest?
This is quite a difficult task becasue the hair goes over your ROI (mole). I don't know how to help remove it from the mole but I can help to remove the backround like in the picture without hairs. For the removal of hairs from mole I advise you to search for "removing of watermarks from image" and "deep neural networks" to maybe train a model to remove the hairs (note that this task will be quite difficult).
That being said, for the removing of background you could try the same code that you allready have for detection without hairs. You will get a binary image like this:
Now your region is filled with white lines (hairs) that go over your contour that is your ROI and cv2.findContours() would also pick them out because they are connected. But if you look at the picture you will find out that the white lines are quite thin and you can remove it from the image by performing opening (cv2.morphologyEx) on the image. Opening is erosion followed by dilation so when you erode the image with a big enough kernel size the white lines will dissapear:
Now you have a white spot with some noises arround which you can connect by performing another dilation (cv2.dilate()):
To make the ROI a bit smoother you can blur the image cv2.blur():
After that you can make another treshold and search for the biggest contour. The final result:
Hope it helps a bit. Cheers!
Example code:
import numpy as np
import cv2
# Read the image and perfrom an OTSU threshold
img = cv2.imread('hair.png')
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
ret, thresh = cv2.threshold(gray,0,255,cv2.THRESH_BINARY_INV+cv2.THRESH_OTSU)
# Remove hair with opening
kernel = np.ones((5,5),np.uint8)
opening = cv2.morphologyEx(thresh,cv2.MORPH_OPEN,kernel, iterations = 2)
# Combine surrounding noise with ROI
kernel = np.ones((6,6),np.uint8)
dilate = cv2.dilate(opening,kernel,iterations=3)
# Blur the image for smoother ROI
blur = cv2.blur(dilate,(15,15))
# Perform another OTSU threshold and search for biggest contour
ret, thresh = cv2.threshold(blur,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
_, contours, hierarchy = cv2.findContours(thresh,cv2.RETR_TREE,cv2.CHAIN_APPROX_NONE)
cnt = max(contours, key=cv2.contourArea)
# Create a new mask for the result image
h, w = img.shape[:2]
mask = np.zeros((h, w), np.uint8)
# Draw the contour on the new mask and perform the bitwise operation
cv2.drawContours(mask, [cnt],-1, 255, -1)
res = cv2.bitwise_and(img, img, mask=mask)
# Display the result
cv2.imshow('img', res)
cv2.waitKey(0)
cv2.destroyAllWindows()