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extract ridges and valleys from finger Image

for my class project I am trying to extract ridges and Valleys from the finger image. An example is given below.
#The code I am using
import cv2
import numpy as np
import fingerprint_enhancer
clip_hist_percent=25
image = cv2.imread("")
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
# Calculate grayscale histogram
hist = cv2.calcHist([gray],[0],None,[256],[0,256])
hist_size = len(hist)
# Calculate cumulative distribution from the histogram
accumulator = []
accumulator.append(float(hist[0]))
for index in range(1, hist_size):
accumulator.append(accumulator[index -1] + float(hist[index]))
# Locate points to clip
maximum = accumulator[-1]
clip_hist_percent *= (maximum/100.0)
clip_hist_percent /= 2.0
# Locate left cut
minimum_gray = 0
while accumulator[minimum_gray] < clip_hist_percent:
minimum_gray += 1
# Locate right cut
maximum_gray = hist_size -1
while accumulator[maximum_gray] >= (maximum - clip_hist_percent):
maximum_gray -= 1
# Calculate alpha and beta values
alpha = 255 / (maximum_gray - minimum_gray)
beta = -minimum_gray * alpha
auto_result = cv2.convertScaleAbs(image, alpha=alpha, beta=beta)
gray = cv2.cvtColor(auto_result, cv2.COLOR_BGR2GRAY)
# compute gamma = log(mid*255)/log(mean)
mid = 0.5
mean = np.mean(gray)
gamma = math.log(mid*255)/math.log(mean)
# do gamma correction
img_gamma1 = np.power(auto_result,gamma).clip(0,255).astype(np.uint8)
g1 = cv2.cvtColor(img_gamma2, cv2.COLOR_BGR2GRAY)
# blur = cv2.GaussianBlur(g1,(2,1),0)
thresh2 = cv2.adaptiveThreshold(g1, 255, cv2.ADAPTIVE_THRESH_GAUSSIAN_C,
cv2.THRESH_BINARY, 199, 3)
# blur = cv2.GaussianBlur(thresh2,(2,1),0)
blur=((3,3),1)
erode_=(5,5)
dilate_=(3, 3)
dilate = cv2.dilate(cv2.erode(cv2.GaussianBlur(thresh2/255, blur[0],
blur[1]), np.ones(erode_)), np.ones(dilate_))*255
out = fingerprint_enhancer.enhance_Fingerprint(dilate)
I am having difficulty extracting the lines on the finger. I tried to adjust the brightness and contrast, applied calcHist, adaptive thresholding, applied blur, then applied the Gabor filters (as per UTKARSH code). The result look like above.
We could clearly see that the lower part of the image has many spurious lines. My project requirement is to get clear lines from the RGB image. Could anyone help me with the steps and the code?
Thank you in advance
reference:
https://github.com/Utkarsh-Deshmukh/Fingerprint-Enhancement-Python
https://ieeexplore.ieee.org/abstract/document/7358782

There are several strange things (IMO) about your code.
First you do a contrast stretch that sets the 12.5% darkest pixels to black and the 12.5% brightest pixels to white. You probably already have this number of white pixels, so not much happens there, but you do remove all the information in the darkest region of the finger print.
Next you threshold. Here you remove most of the remaining information. Thresholding is something you should leave until the very last step of any processing. In particular, the algorithm implemented in fingerprint_enhancer.enhance_Fingerprint() takes a gray-scale image as input. You should not binarize its input at all!
I would start with a local contrast stretch, then you can directly apply the enhancement algorithm:
import cv2
import fingerprint_enhancer
image = cv2.imread("zMxbO.jpg")
gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
# Apply local contrast stretch
se = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (25, 25)) # larger than the width of the widest ridges
low = cv2.morphologyEx(gray, cv2.MORPH_OPEN, se) # locally lowest grayvalue
high = cv2.morphologyEx(gray, cv2.MORPH_CLOSE, se) # locally highest grayvalue
gray = (gray - o) / (c - o + 1e-6)
# Apply fingerprint enhancement
out = fingerprint_enhancer.enhance_Fingerprint(gray, resize=True)
The local contrast stretch yields this:
The finger print enhancement algorithm now yields this:
Note things go wrong around the edges, where the background was cut out and replaced with white, as well as in the dark region, where the noise dominates and the enhancement algorithm hallucinates a bit. I don't think you can extract meaningful information from that area, a better illumination would be necessary.

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

Opencv, Python - How to remove the gray pixels around the date text

I am trying to remove the grayish “noise” surrounding the dates using Python/OpenCV to help the OCR (Optical Character Recognition) to recognize the dates.
The original image looks like this: https://static.mothership.sg/1/2017/03/10-Feb-MC-1.jpg
The python script I tried looked as below. However, I have other similar images in which the contrast or lighting coditions varies.
import cv2
import numpy as np
img = cv2.imread("mc.jpeg")
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
alpha = 3.5
beta = -2
new = alpha * img + beta
new = np.clip(new, 0, 255).astype(np.uint8)
cv2.imwrite("cleaned.png", new)
I also tried Thresholding and/or adaptiveThresholding and some time, I was able to separate the dates from the grayish background. Sometimes it was very challenging. I wonder is there an automatic way to determine the threshold value ?
Below are example of what I hope to achieve.
Blurry Image:

Otsu's Binarization automatically calculates a threshold value from an image histogram.
# Otsu's thresholding after Gaussian filtering
blur = cv2.GaussianBlur(img,(5,5),0)
ret,Otsu = cv2.threshold(blur,0,255,cv2.THRESH_BINARY+cv2.THRESH_OTSU)
cv2.imwrite("Otsu's_thresholding", Otsu)
see this link

You can try to build a model of the background and then weight each input pixel by that model. The output gain should be relatively constant during most of the image. These are the steps for this method:
Apply a soft median blur filter to get rid of small noise
Get the model of the background via local maximum. Apply a very strong close operation, with a big structuring element (I’m using a rectangular kernel of size 15)
Perform gain adjustment by dividing 255 between each local maximum pixel. Weight this value with each input image pixel.
You should get a nice image where the background illumination is pretty much normalized, threshold this image to get a binary mask of the text
This is the code:
import numpy as np
import cv2
# image path
path = "C:/opencvImages/sheet01.jpg"
# Read an image in default mode:
inputImage = cv2.imread(path)
# Remove small noise via median:
filterSize = 5
imageMedian = cv2.medianBlur(inputImage, filterSize)
# Get local maximum:
kernelSize = 15
maxKernel = cv2.getStructuringElement(cv2.MORPH_RECT, (kernelSize, kernelSize))
localMax = cv2.morphologyEx(imageMedian, cv2.MORPH_CLOSE, maxKernel, None, None, 1, cv2.BORDER_REFLECT101)
# Adjust image gain:
height, width, depth = localMax.shape
# Create output Mat:
outputImage = np.zeros(shape=[height, width, depth], dtype=np.uint8)
for i in range(0, height):
for j in range(0, width):
# Get current BGR pixels:
v1 = inputImage[i, j]
v2 = localMax[i, j]
# Gain adjust:
tempArray = []
for c in range(0, 3):
currentPixel = v2[c]
if currentPixel != 0:
gain = 255 / v2[c]
gain = v1[c] * gain
else:
gain = 0
# Gain set and clamp:
tempArray.append(np.clip(gain, 0, 255))
# Set pixel vec to out image:
outputImage[i, j] = tempArray
# Convert RGB to grayscale:
grayscaleImage = cv2.cvtColor(outputImage, cv2.COLOR_BGR2GRAY)
# Threshold:
threshValue = 110
_, binaryImage = cv2.threshold(grayscaleImage, threshValue, 255, cv2.THRESH_BINARY)
# Write image:
imageFilename = "C:/opencvImages/binaryMask2.png"
cv2.imwrite(imageFilename, binaryImage)
I get the following results testing the complete image:
And the cropped text:
Please note that the gain adjustment operations are not vectorized. The script is slow, mainly because I'm starting with Python and don’t know the proper Numpy syntax to speed-up this operation. I've been using C++ for a long time, so feel free to further improve the code.
Edit:
Please, be aware that your result can only be as good as the quality of your input. See your input and ask yourself "Is this a good input for an automated process?" (Automated processes are usually not very smart). The second picture you posted is very low quality. Not only is blurry but also is low res and has compression artifacts. All these factors will hinder automated processing.
With that said, here's an improvement you can include in the original:
Try to normalize brightness-contrast on the grayscale output:
grayscaleImage = np.uint8(cv2.normalize(grayscaleImage, grayscaleImage, 0, 255, cv2.NORM_MINMAX))
Your grayscale image goes from this:
to this:
A little bit darker and improved on contrast. Let's try to compute the optimal threshold value automatically via Otsu thresholding:
threshValue, binaryImage = cv2.threshold(grayscaleImage, 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
It gets you this:
However, we can adjust the result if we add bias to Otsu's threshold, like this:
threshValue, binaryImage = cv2.threshold(grayscaleImage, 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
bias = 0.9
threshValue = bias * threshValue
_, binaryImage = cv2.threshold(grayscaleImage, threshValue, 255, cv2.THRESH_BINARY)
That's the best quality you can get with these images using this method.
If you find these suggestions and tips useful, please, at least up-vote my answer.

image analysis (opencv or scikit image), deskewing of noisy scan

I do have some old bank statements as scan and would like to use google´s thesseract engine to extract the text. Works pretty well unless the image is slightly rotated. I thought of detecting the dashed lines in order to estimate the slope and afterwards the angle of rotation. However, it is tricky to get the parameters right.
If I could get rid of the large line artefact, I might use the minimum rotated bounding box (cv2.minAreaRect) on the text characters.
Maybe another strategy is suited better ? Any ideas ?
An example image (deleted some characters for data protection):
EIDT: I have found a solution which seems to work. However, I am stil wondering if there might be a faster solution (takes about 1.5 seconds per Image)
I do use template matching from skimage with following template:
template = plt.imread('template_long.png')
template = rgb2gray(template)
template = template > threshold_mean(template)
for i in range(1):
# read in image
img = cv2.imread('conversion/umsatz_{}.png'.format(i))
# convert to grayscale
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
gray = cv2.bitwise_not(gray)
# threshold the image, setting all foreground pixels to
# 255 and all background pixels to 0
thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY | cv2.THRESH_OTSU)[1]
# edge detection
#edges = cv2.Canny(thresh,2,100, apertureSize = 3)
# fill the holes from detected edges
#kernel = np.ones((2,2),np.uint8)
#dilate = cv2.dilate(thresh, kernel, iterations=1)
result = match_template(thresh, template)
mask = result < 0.5
r = result.copy()
r[mask] = 0
r[~mask] = 1
plt.imshow(r)

Remove features from binarized image

I wrote a little script to transform pictures of chalkboards into a form that I can print off and mark up.
I take an image like this:
Auto-crop it, and binarize it. Here's the output of the script:
I would like to remove the largest connected black regions from the image. Is there a simple way to do this?
I was thinking of eroding the image to eliminate the text and then subtracting the eroded image from the original binarized image, but I can't help thinking that there's a more appropriate method.

Sure you can just get connected components (of certain size) with findContours or floodFill, and erase them leaving some smear. However, if you like to do it right you would think about why do you have the black area in the first place.
You did not use adaptive thresholding (locally adaptive) and this made your output sensitive to shading. Try not to get the black region in the first place by running something like this:
Mat img = imread("desk.jpg", 0);
Mat img2, dst;
pyrDown(img, img2);
adaptiveThreshold(255-img2, dst, 255, ADAPTIVE_THRESH_MEAN_C,
THRESH_BINARY, 9, 10); imwrite("adaptiveT.png", dst);
imshow("dst", dst);
waitKey(-1);
In the future, you may read something about adaptive thresholds and how to sample colors locally. I personally found it useful to sample binary colors orthogonally to the image gradient (that is on the both sides of it). This way the samples of white and black are of equal size which is a big deal since typically there are more background color which biases estimation. Using SWT and MSER may give you even more ideas about text segmentation.

I tried this:
import numpy as np
import cv2
im = cv2.imread('image.png')
gray = cv2.cvtColor(im,cv2.COLOR_BGR2GRAY)
grayout = 255*np.ones((im.shape[0],im.shape[1],1), np.uint8)
blur = cv2.GaussianBlur(gray,(5,5),1)
thresh = cv2.adaptiveThreshold(blur,255,1,1,11,2)
contours,hierarchy = cv2.findContours(thresh,cv2.RETR_LIST,cv2.CHAIN_APPROX_SIMPLE)
wcnt = 0
for item in contours:
area =cv2.contourArea(item)
print wcnt,area
[x,y,w,h] = cv2.boundingRect(item)
if area>10 and area<200:
roi = gray[y:y+h,x:x+w]
cntd = 0
for i in range(x,x+w):
for j in range(y,y+h):
if gray[j,i]==0:
cntd = cntd + 1
density = cntd/(float(h*w))
if density<0.5:
for i in range(x,x+w):
for j in range(y,y+h):
grayout[j,i] = gray[j,i];
wcnt = wcnt + 1
cv2.imwrite('result.png',grayout)
You have to balance two things, removing the black spots but balance that with not losing the contents of what is on the board. The output I got is this:

Here is a Python numpy implementation (using my own mahotas package) of the method for the top answer (almost the same, I think):
import mahotas as mh
import numpy as np
Imported mahotas & numpy with standard abbreviations
im = mh.imread('7Esco.jpg', as_grey=1)
Load the image & convert to gray
im2 = im[::2,::2]
im2 = mh.gaussian_filter(im2, 1.4)
Downsample and blur (for speed and noise removal).
im2 = 255 - im2
Invert the image
mean_filtered = mh.convolve(im2.astype(float), np.ones((9,9))/81.)
Mean filtering is implemented "by hand" with a convolution.
imc = im2 > mean_filtered - 4
You might need to adjust the number 4 here, but it worked well for this image.
mh.imsave('binarized.png', (imc*255).astype(np.uint8))
Convert to 8 bits and save in PNG format.