We Keep Coding

How can I remove these parallel lines noise on my image using opencv

I'm new to opencv and I m trying to remove all these diagonal parallel lines that are noise in my image.
I have tried using HoughLinesP after some erosion/dilatation but the result is poo (and keeping only the one with a near 135 degree angle).
img = cv2.imread('images/dungeon.jpg')
ret,img = cv2.threshold(img,180,255,0)
element = cv2.getStructuringElement(cv2.MORPH_CROSS,(5,5))
eroded = cv2.erode(img,element)
dilate = cv2.dilate(eroded, element)
skeleton = cv2.subtract(img, dilate)
gray = cv2.cvtColor(skeleton,cv2.COLOR_BGR2GRAY)
minLineLength = 10
lines = cv2.HoughLinesP(gray, 1, np.pi/180, 1, 10, 0.5)
for line in lines:
for x1,y1,x2,y2 in line:
angle = math.atan2(y2-y1,x2-x1)
if (angle > -0.1 and angle < 0.1):
cv2.line(img,(x1,y1),(x2,y2),(0,255,0),1)
cv2.imshow("result", img)
cv2.waitKey(0)
cv2.destroyAllWindows()
My thinking here was to detect these lines in order to remove them afterwards but I m not even sure that's the good way to do this.

I guess you are trying to get the contours of the walls, right? Here’s a possible path to the solution using mainly spatial filtering. You will still need to clean the results to get where you want. The idea is to try and compute a mask of the parallel lines (high-frequency noise) of the image and calculate the difference between the (binary) input and this mask. These are the steps:
Convert the input image to grayscale
Apply Gaussian Blur to get rid of the high-frequency noise you are trying to eliminate
Get a binary image of the blurred image
Apply area filters to get rid of everything that is not noise, to get a noise mask
Compute the difference between the original binary mask and the noise mask
Clean up the difference image
Compute contours on this image
Let’s see the code:
import cv2
import numpy as np
# Set image path
path = "C://opencvImages//"
fileName = "map.png"
# Read Input image
inputImage = cv2.imread(path+fileName)
# Convert BGR to grayscale:
grayscaleImage = cv2.cvtColor(inputImage, cv2.COLOR_BGR2GRAY)
# Apply Gaussian Blur:
blurredImage = cv2.GaussianBlur(grayscaleImage, (3, 3), cv2.BORDER_DEFAULT)
# Threshold via Otsu:
_, binaryImage = cv2.threshold(blurredImage, 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
# Save a copy of the binary mask
binaryCopy = cv2.cvtColor(binaryImage, cv2.COLOR_GRAY2BGR)
This is the output:
Up until now you get this binary mask. The process so far has smoothed the noise and is creating thick black blobs where the noise is located. Again, the idea is to generate a noise mask that can be subtracted to this image.
Let’s apply an area filter and try to remove the big white blobs, which are NOT the noise we are interested to preserve. I’ll define the function towards the end, for now I just want to present the general idea:
# Set the minimum pixels for the area filter:
minArea = 50000
# Perform an area filter on the binary blobs:
filteredImage = areaFilter(minArea, binaryImage)
The filter will suppress every white blob that is above the minimum threshold. The value is big because in this particular case we are interested in preserving only the black blobs. This is the result:
We have a pretty solid mask. Let’s subtract this from the original binary mask we created earlier:
# Get the difference between the binary image and the mask:
imgDifference = binaryImage - filteredImage
This is what we get:
The difference image has some small noise. Let’s apply the area filter again to get rid of it. This time with a more traditional threshold value:
# Set the minimum pixels for the area filter:
minArea = 20
# Perform an area filter on the binary blobs:
filteredImage = areaFilter(minArea, imgDifference)
Cool. This is the final mask:
Just for completeness. Let’s compute contours on this input, which is very straightforward:
# Find the big contours/blobs on the filtered image:
contours, hierarchy = cv2.findContours(filteredImage, cv2.RETR_CCOMP, cv2.CHAIN_APPROX_SIMPLE)
# Draw the contours on the mask image:
cv2.drawContours(binaryCopy, contours, -1, (0, 255, 0), 3)
Let’s see the result:
As you see it is not perfect. However, there’s still some room for improvement, perhaps you can polish a little bit more this idea to get a potential solution. Here's the definition and implementation of the areaFilter function:
def areaFilter(minArea, inputImage):
# Perform an area filter on the binary blobs:
componentsNumber, labeledImage, componentStats, componentCentroids = \
cv2.connectedComponentsWithStats(inputImage, connectivity=4)
# Get the indices/labels of the remaining components based on the area stat
# (skip the background component at index 0)
remainingComponentLabels = [i for i in range(1, componentsNumber) if componentStats[i][4] >= minArea]
# Filter the labeled pixels based on the remaining labels,
# assign pixel intensity to 255 (uint8) for the remaining pixels
filteredImage = np.where(np.isin(labeledImage, remainingComponentLabels) == True, 255, 0).astype('uint8')
return filteredImage

How masking is applied in bitwise_operation in opencv?

I was looking at the documentation of the OpenCV and found something which I couldn't understand. I've tried to find it on the web but couldn't find anything satisfying. Can you please help me in a line of code?
Here is the code:
# Load two images
img1 = cv.imread('messi5.jpg')
img2 = cv.imread('opencv-logo-white.png')
# I want to put logo on top-left corner, So I create a ROI
rows,cols,channels = img2.shape
roi = img1[0:rows, 0:cols ]
# Now create a mask of logo and create its inverse mask also
img2gray = cv.cvtColor(img2,cv.COLOR_BGR2GRAY)
ret, mask = cv.threshold(img2gray, 10, 255, cv.THRESH_BINARY)
mask_inv = cv.bitwise_not(mask)
# Now black-out the area of logo in ROI
img1_bg = cv.bitwise_and(roi,roi,mask = mask_inv)
# Take only region of logo from logo image.
img2_fg = cv.bitwise_and(img2,img2,mask = mask)
# Put logo in ROI and modify the main image
dst = cv.add(img1_bg,img2_fg)
img1[0:rows, 0:cols ] = dst
cv.imshow('res',img1)
cv.waitKey(0)
cv.destroyAllWindows()
What I actually don't understand are these two lines
img1_bg = cv.bitwise_and(roi,roi,mask = mask_inv)
img2_fg = cv.bitwise_and(img2,img2,mask = mask)
What these lines actually do and how the masking will be applied?
If anyone can explain the masking being applied in the bitwise_and operation that would be really helpful.Thanks

If you look at the tutorial.
The mask is the black and white image of the OpenCV logo, it was created from applying a threshold to the OpenCV logo.
The bitwise_and operation is a logical and operation
In this case, it is taking two 8 bit numbers representing a pixel and applying the and operation on those numbers.
Documentation describes what this function does.
Since the first two parameters are the same (both roi or img2) the result would be the same image if a mask wasn't being used. Places, where the mask is black, are left the same as the destination image.
In this case, no destination image is provided, so OpenCV allocates a black image (zeros) for the destination image used in the function (this is generally how OpenCV works when a function is not provided with a Matrix).
Specifically img1_bg = cv.bitwise_and(roi,roi,mask = mask_inv) will create a black matrix used in the function which later becomes the output img1_bg. Only the parts of this black image that match up with white pixels in mask_inv are filled with the pixels from roi.This means that in the mask_inv where there are white pixels. the roi value will be copied in the pure black image generated by the function in the corresponding coordinate.
Similarly img2_fg = cv.bitwise_and(img2,img2,mask = mask) will create a black matrix used in the function which later becomes the output img2_fg. Only the parts of this black image that match up with white pixels in mask are filled with the pixels from img2.
This makes it so when you add img1_bg and img2_fg the result is only the part of each image that is masked.
Personally, I think this is a confusing use of bitwise_and. I think to demonstrate the function of bitwise_and it would be clearer to remove the mask parameter as follows: img1_bg = cv.bitwise_and(roi, mask_inv). This would give the same result, zeros where the mask is black, and the ROI values where it is not since the mask has pixels that are all ones or all zeroes.
If you don't care to demonstrate bitwise_and usage, in python I think it would be clearer to use logical indexing as follows:
output = np.zeros(img1.shape, np.uint8)
output[mask_inv] = img1_bg[mask_inv]
output[mask] = img2_fg[mask]

How to remove hair from skin images using opencv?

I am working with recognition of skin spots. For this, I work with a number of images with different noises. One of these noises are the hairs, because I have images with hairs over the area of ​​the stain (ROI). How to decrease or remove these types of image noise?
The code below decreases the area where hairs are, but does not remove hairs that are above the area of ​​interest (ROI).
import numpy as np
import cv2
IMD = 'IMD436'
# Read the image and perfrom an OTSU threshold
img = cv2.imread(IMD+'.bmp')
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((2,2),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.imwrite(IMD+'.png', res)
cv2.imshow('img', res)
cv2.waitKey(0)
cv2.destroyAllWindows()
Exit:
How can I remove hair from the top of my region of interest?
Images used:

I am responding to your tag on a related post. As I understand you and another colege are working together on a project to locate the moles on the skin? Because I think I have already gave help to one or maybe both of you on similar questions and already mentioned that the removal of the hair is very tricky and difficult task. If you remove the hair on the image you lose information and you can't replace that part of the image (no program or alghorithm can guess what is under the hair - but it can make an estimation). What you could do as I mentioned in other posts and I think that it would be the best approach is to learn about deep neural networks and make your own for the hair removal. You can google "watermark removal deep neural network" and see what I mean. That being said, your code does not seem to extract all ROIs (the moles) you have given in the example image. I have made another example on how you can better extract the moles. Basically you should perform closing before transforming to binary and you will get better results.
For the second part - hair removal, if you do not wish to make a neural network, I think that alternative solution could be, that you calculate the mean pixel intesity of the region that contains the mole. Then iterate throug every pixel and make some sort of criteria on how much can the pixel differ from the mean. Hair seem to be presented with pixels that are darker than the mole area. So when you find the pixel, replace it with the neigbour pixel that does not fall in this criteria. In the example I have made a simple logic which will not work with every image but it can serve as an example. To make a fully operational solution you should make a better, more complex alghorithm which I guess will take quite some time. Hope it helps a bit! Cheers!
import numpy as np
import cv2
from PIL import Image
# Read the image and perfrom an OTSU threshold
img = cv2.imread('skin2.png')
kernel = np.ones((15,15),np.uint8)
# Perform closing to remove hair and blur the image
closing = cv2.morphologyEx(img,cv2.MORPH_CLOSE,kernel, iterations = 2)
blur = cv2.blur(closing,(15,15))
# Binarize the image
gray = cv2.cvtColor(blur,cv2.COLOR_BGR2GRAY)
_, thresh = cv2.threshold(gray,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)
# Calculate the mean color of the contour
mean = cv2.mean(res, mask = mask)
print(mean)
# Make some sort of criterion as the ratio hair vs. skin color varies
# thus makes it hard to unify the threshold.
# NOTE that this is only for example and it will not work with all images!!!
if mean[2] >182:
bp = mean[0]/100*35
gp = mean[1]/100*35
rp = mean[2]/100*35
elif 182 > mean[2] >160:
bp = mean[0]/100*30
gp = mean[1]/100*30
rp = mean[2]/100*30
elif 160>mean[2]>150:
bp = mean[0]/100*50
gp = mean[1]/100*50
rp = mean[2]/100*50
elif 150>mean[2]>120:
bp = mean[0]/100*60
gp = mean[1]/100*60
rp = mean[2]/100*60
else:
bp = mean[0]/100*53
gp = mean[1]/100*53
rp = mean[2]/100*53
# Write temporary image
cv2.imwrite('temp.png', res)
# Open the image with PIL and load it to RGB pixelpoints
mask2 = Image.open('temp.png')
pix = mask2.load()
x,y = mask2.size
# Itearate through the image and make some sort of logic to replace the pixels that
# differs from the mean of the image
# NOTE that this alghorithm is for example and it will not work with other images
for i in range(0,x):
for j in range(0,y):
if -1<pix[i,j][0]<bp or -1<pix[i,j][1]<gp or -1<pix[i,j][2]<rp:
try:
pix[i,j] = b,g,r
except:
pix[i,j] = (int(mean[0]),int(mean[1]),int(mean[2]))
else:
b,g,r = pix[i,j]
# Transform the image back to cv2 format and mask the result
res = np.array(mask2)
res = res[:,:,::-1].copy()
final = cv2.bitwise_and(res, res, mask=mask)
# Display the result
cv2.imshow('img', final)
cv2.waitKey(0)
cv2.destroyAllWindows()

You can try the following steps, at least to get a road map to the proper solution implementation:
Find the hair region using adaptive local thresholding - Otsu's
method or any other method. I think "local thresholding" or even
"local histogram equalization and then global thresholding" will
find the hair regions.
To fill the hair regions, use "texture synthesis" to synthesize skin
like texture for the hair region.
One good and easy method for texture synthesis is described in "A.A. Efros and T.K. Leung, Texture synthesis by non-parametric sampling', In Proceedings of the International Conference on Computer Vision (ICCV), Kerkyra, Greece, 1999".
Texture synthesis will give a better result than averaging or median filtering to estimate the pixels in the hair region.
Also, take a look at this paper, it should help you a lot:
http://link.springer.com/article/10.1007%2Fs00521-012-1149-1?LI=true

Normalizing images in OpenCV produces black image?

I wrote the following code to normalize an image using NORM_L1 in OpenCV. But the output image was just black. How to solve this?
import cv2
import numpy as np
import Image
img = cv2.imread('img7.jpg')
gray_image = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
a = np.asarray(gray_image)
dst = np.zeros(shape=(5,2))
b=cv2.normalize(a,dst,0,255,cv2.NORM_L1)
im = Image.fromarray(b)
im.save("img50.jpg")
cv2.waitKey(0)
cv2.destroyAllWindows()

If you want to change the range to [0, 1], make sure the output data type is float.
image = cv2.imread("lenacolor512.tiff", cv2.IMREAD_COLOR) # uint8 image
norm_image = cv2.normalize(image, None, alpha=0, beta=1, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_32F)

The other answers normalize an image based on the entire image. But if your image has a predominant color (such as black), it will mask out the features that you're trying to enhance since it will not be as pronounced. To get around this limitation, we can normalize the image based on a subsection region of interest (ROI). Essentially we will normalize based on the section of the image that we want to enhance instead of equally treating each pixel with the same weight. Take for instance this earth image:
Input image -> Normalization based on entire image
If we want to enhance the clouds by normalizing based on the entire image, the result will not be very sharp and will be over saturated due to the black background. The features to enhance are lost. So to obtain a better result we can crop a ROI, normalize based on the ROI, and then apply the normalization back onto the original image. Say we crop the ROI highlighted in green:
This gives us this ROI
The idea is to calculate the mean and standard deviation of the ROI and then clip the frame based on the lower and upper range. In addition, we could use an offset to dynamically adjust the clip intensity. From here we normalize the original image to this new range. Here's the result:
Before -> After
Code
import cv2
import numpy as np
# Load image as grayscale and crop ROI
image = cv2.imread('1.png', 0)
x, y, w, h = 364, 633, 791, 273
ROI = image[y:y+h, x:x+w]
# Calculate mean and STD
mean, STD = cv2.meanStdDev(ROI)
# Clip frame to lower and upper STD
offset = 0.2
clipped = np.clip(image, mean - offset*STD, mean + offset*STD).astype(np.uint8)
# Normalize to range
result = cv2.normalize(clipped, clipped, 0, 255, norm_type=cv2.NORM_MINMAX)
cv2.imshow('image', image)
cv2.imshow('ROI', ROI)
cv2.imshow('result', result)
cv2.waitKey()
The difference between normalizing based on the entire image vs a specific section of the ROI can be visualized by applying a heatmap to the result. Notice the difference on how the clouds are defined.
Input image -> heatmap
Normalized on entire image -> heatmap
Normalized on ROI -> heatmap
Heatmap code
import matplotlib.pyplot as plt
import numpy as np
import cv2
image = cv2.imread('result.png', 0)
colormap = plt.get_cmap('inferno')
heatmap = (colormap(image) * 2**16).astype(np.uint16)[:,:,:3]
heatmap = cv2.cvtColor(heatmap, cv2.COLOR_RGB2BGR)
cv2.imshow('image', image)
cv2.imshow('heatmap', heatmap)
cv2.waitKey()
Note: The ROI bounding box coordinates were obtained using how to get ROI Bounding Box Coordinates without Guess & Check and heatmap code was from how to convert a grayscale image to heatmap image with Python OpenCV

When you normalize a matrix using NORM_L1, you are dividing every pixel value by the sum of absolute values of all the pixels in the image.
As a result, all pixel values become much less than 1 and you get a black image. Try NORM_MINMAX instead of NORM_L1.

OpenCV via python: Is there a fast way to zero pixels outside a set of rectangles?

I have an image of a face and I have used haar cascades to detect the locations (x,y,width,height) of the mouth, nose and each eye. I would like to set all pixels outside these regions to zero. What would be the fastest (computationally) way to do this? I'll eventually be doing it to video frames in real time.

I don't know whether it is the fastest way, but It is a way to do it.
Create a mask image with region of face as white, then apply bitwise_and function with original image and mask image.
x = y = 30
w = h = 100
mask = np.zeros(img.shape[:2],np.uint8)
mask[y:y+h,x:x+w] = 255
res = cv2.bitwise_and(img,img,mask = mask)
It takes 0.16 ms in my system (core i5,4GB RAM) for an image of size 400x300
EDIT - BETTER METHOD: You need not do as above. Simply create a zero image and then copy ROI from original image to zero image. that's all.
mask = np.zeros(img.shape,np.uint8)
mask[y:y+h,x:x+w] = img[y:y+h,x:x+w]
It takes only 0.032 ms in my system for above parameters, 5 times faster than above.
Results :
Input Image :
Output :

If a polygon ROI is to be made.
Create the polygon and make a mask for it. Multiply the image with the created frame.
ret,frame = cv2.imread()
xr=1
yr=1
# y,x
pts = np.array([[int(112*yr),int(32*xr)],[int(0*yr),int(623*xr)],[int(789*yr),int(628*xr)],[int(381*yr),int(4*xr)]], np.int32)
pts = pts.reshape((-1,1,2))
cv2.polylines(frame,[pts],True,(0,255,255))
mask = np.zeros(frame.shape[:2],np.uint8)
cv2.fillPoly(mask,[pts],(255,255,255))
frame = cv2.bitwise_and(frame,frame,mask = mask)
cv2.imshow("masked frame", frame)