How to disconnect adjoined regions using morphology without losing information - python

I have a 3d image which is the segmentation result of a input volume, the system works fine except for when two cells are located very close to each other, then in that case the segmentation results come back as the two cells joined as shown in the image below:
The circled are are actually two cells but are joined combined due to being closely located. In CC counting these two come up as a single cell.
I tried using morphological opening but it does not seem to provide the result I want. With a single iteration I have no effect ad with enough iterations to break the gap, I lose the smaller blobs.
import imageio as io
import numpy as np
import skimage.morphology as morph
import scipy.ndimage as ndimage
img = io.volread('test_volumes/volume_4_1_predictions.tif')
bw_img = img > 0.5 # binrize image
bw_img = 1 - bw_img # this changes True False to 1 and 0
bw_img = 1 - bw_img # Make background black and foreground white
strel = morph.ball(1)
opened = ndimage.binary_opening(opened, strel, 5)
5 iterations of this opens the gap but i seem to lose a lot of information.
Erosion does not work either as it loses more information than opening.
What would be the best way to disconnect these two cells?
Here is the 3d image in.tif format: https://app.box.com/s/9wcqf3qbn8d9jg8zfvw3ijz85baes8t4

Related

How to Improve OCR on image with text in different colors and fonts?

I'm using the Google Vision API to extract the text from some pictures, however, I have been trying to improve the accuracy (confidence) of the results with no luck.
every time I change the image from the original I lose accuracy in detecting some characters.
I have isolated the issue to have multiple colors for different words with can be seen that words in red for example have incorrect results more often than the other words.
Example:
some variations on the image from gray scale or b&w
What ideas can I try to make this work better, specifically changing the colors of text to a uniform color or just black on a white background since most algorithms expect that?
some ideas I already tried, also some thresholding.
dimg = ImageOps.grayscale(im)
cimg = ImageOps.invert(dimg)
contrast = ImageEnhance.Contrast(dimg)
eimg = contrast.enhance(1)
sharp = ImageEnhance.Sharpness(dimg)
eimg = sharp.enhance(1)
I can only offer a butcher's solution, potentially a nightmare to maintain.
In my own, very limited scenario, it worked like a charm where several other OCR engines either failed or had unacceptable running times.
My prerequisites:
I knew exactly in which area of the screen the text was going to go.
I knew exactly which fonts and colors were going to be used.
the text was semitransparent, so the underlying image interfered, and it was a variable image to boot.
I could not detect reliably text changes to average frames and reduce the interference.
What I did:
- I measured the kerning width of each character. I only had A-Za-z0-9 and a bunch of punctuation characters to worry about.
- The program would start at position (0,0), measure the average color to determine the color, then access the whole set of bitmaps generated from characters in all available fonts in that color. Then it would determine which rectangle was closest to the corresponding rectangle on the screen, and advance to the next one.
(Months later, requiring more performances, I added a varying probability matrix to test first the most likely characters).
In the end, the resulting C program was able to read the subtitles out of the video stream with 100% accuracy in real time.
You tried almost every standard step. I would advise you to try some PIL built-in filters like sharpness filter. Apply sharpness and contrast on the RGB image, then binarise it. Perhaps use Image.split() and Image.merge() to binarise each colour separately and then bring them back together.
Or convert your image to YUV and then use just Y channel for further processing.
Also, if you do not have a monochrome background consider performing some background substraction.
What tesseract likes when detecting scanned text is removed frames, so you can try to destroy as much of non character space from the image. (You might need to keep the picture size though, so you should replace it with white colour). Tesseract also likes straight lines. So some deskewing might be in order if your text is recorded at an angle. Tesseract also sometimes gives better results if you resize the image to twice its original size.
I suspect that Google Vision uses tesseract, or portions of it, but what other preprocessing it does for you I have no idea. So some of my advices here might actually be implemented already and doing them would be unnecessary and repetitive.
You will need to pre-process the image more than once, and use a bitwise_or operation to combine the results. To extract the colors, you could use
import cv2
boundaries = [ #BGR colorspace for opencv, *not* RGB
([15, 15, 100], [50, 60, 200]), #red
([85, 30, 2], [220, 90, 50]), #blue
([25, 145, 190], [65, 175, 250]), #yellow
]
for (low, high) in boundaries:
low = np.array(low, dtype = "uint8")
high = np.array(high, dtype = "uint8")
# find the colors within the specified boundaries and apply
# the mask
mask = cv2.inRange(image, low, high)
bitWise = cv2.bitwise_and(image, image, mask=mask)
#now here is the image masked with the specific color boundary...
Once you have the masked image, you can do another bitwise_or operation on your to-be "final" image, essentially adding this mask to it.
but this specific implementation requires opencv, however the same principle applies for other image packages.
I need a little more context on this.
How many calls are you going to do to the Google Vision API? If you are doing this throughout a whole stream, you'd probably need to get a paid subscription.
What are you going to do with this data? How accurate does the OCR need to be?
Assuming you get this snapshot from another's twitch stream, dealing with the streamer's video compression and network connectivity, you're going to get pretty blurry snapshot, so OCR is going to be pretty tough.
The image is far too blurry because of video compression, so even preprocessing the image to improve quality may not get the image quality high enough for accurate OCR. If you are set on OCR, one approach you could try:
Binarize the image to get the non-red text in white and background black as in your binarized image:
from PIL import Image
def binarize_image(im, threshold):
"""Binarize an image."""
image = im.convert('L') # convert image to monochrome
bin_im = image.point(lambda p: p > threshold and 255)
return bin_im
im = Image.open("game_text.JPG")
binarized = binarize_image(im, 100)
Extract only the red text values with a filter, then binarize it:
import cv2
from matplotlib import pyplot as plt
lower = [15, 15, 100]
upper = [50, 60, 200]
lower = np.array(lower, dtype = "uint8")
upper = np.array(upper, dtype = "uint8")
mask = cv2.inRange(im, lower, upper)
red_binarized = cv2.bitwise_and(im, im, mask = mask)
plt.imshow(cv2.cvtColor(red_binarized, cv2.COLOR_BGR2RGB))
plt.show()
However, even with this filtering, it still doesn't extract red well.
Add images obtained in (1.) and (2.).
combined_image = binarized + red_binarized
Do OCR on (3.)
This is not a full solution but it may drive to something better.
By converting your data from BGR (or RGB) to CIE-Lab you can process a grayscale image as the weighted sum of the colour channels a* and b*.
This grayscale image will enhance colour regions of the text.
But adapting the threshold you can from this grayscale image segment the coloured word in your original image and get the other words from the a L channel thresholding.
A bitwise and operator should be enough to merge to two segmentation image.
If you can have an image with a better contrast a very last step could be a filling based on the contours.
For that take a look to RETR_FLOODFILL of the function 'cv2.findContours'.
Any other hole filing function from other package may also fit for that purpose.
Here is a code that show the first part of my idea.
import cv2
import numpy as np
from matplotlib import pyplot as plt
I = cv2.UMat(cv2.imread('/home/smile/QSKN.png',cv2.IMREAD_ANYCOLOR))
Lab = cv2.cvtColor(I,cv2.COLOR_BGR2Lab)
L,a,b = cv2.split(Lab)
Ig = cv2.addWeighted(cv2.UMat(a),0.5,cv2.UMat(b),0.5,0,dtype=cv2.CV_32F)
Ig = cv2.normalize(Ig,None,0.,255.,cv2.NORM_MINMAX,cv2.CV_8U)
#k = np.ones((3,3),np.float32)
#k[2,2] = 0
#k*=-1
#
#Ig = cv2.filter2D(Ig,cv2.CV_32F,k)
#Ig = cv2.absdiff(Ig,0)
#Ig = cv2.normalize(Ig,None,0.,255.,cv2.NORM_MINMAX,cv2.CV_8U)
_, Ib = cv2.threshold(Ig,0.,255.,cv2.THRESH_OTSU)
_, Lb = cv2.threshold(cv2.UMat(L),0.,255.,cv2.THRESH_OTSU)
_, ax = plt.subplots(2,2)
ax[0,0].imshow(Ig.get(),cmap='gray')
ax[0,1].imshow(L,cmap='gray')
ax[1,0].imshow(Ib.get(),cmap='gray')
ax[1,1].imshow(Lb.get(),cmap='gray')
import numpy as np
from skimage.morphology import selem
from skimage.filters import rank, threshold_otsu
from skimage.util import img_as_float
from PIL import ImageGrab
import matplotlib.pyplot as plt
def preprocessing(image, strelem, s0=30, s1=30, p0=.3, p1=1.):
image = rank.mean_bilateral(image, strelem, s0=s0, s1=s1)
condition = (lambda x: x>threshold_otsu(x))(rank.maximum(image, strelem))
normalize_image = rank.autolevel_percentile(image, strelem, p0=p0, p1=p1)
return np.where(condition, normalize_image, 0)
#Grab image from clipboard
image = np.array(ImageGrab.grabclipboard())
sel = selem.disk(4)
a = sum([img_as_float(preprocessing(image[:, :, x], sel, p0=0.3)) for x in range(3)])/3
fig, ax = plt.subplots(1, 2, sharey=True, sharex=True)
ax[0].imshow(image)
ax[1].imshow(rank.autolevel_percentile(a, sel, p0=.4))
This is my code for clearing text from noise and creating uniform brightness for characters.
With minor modifications, I used it to solve your problem.

Difficulty in detected ellipses in image

I am trying to detect ellipses in some images.
After some functions I got this edges map:
I tried using Hough transform to detect ellipses, but this transform has very high complexity, so my computer didn't finish running the transform command even after 5 hours(!).
I also tried doing connected components and got this:
In last case I also tried continue and binarized the image.
In all cases I am stuck in these steps, and have no idea how continue from here.
My mission is detect tomatoes in the image. I am approaching this by trying to detect circles and ellipses and find the radius (or average radius in ellipses case) for each one.
edited:
I add my code for the first method (the result is edge map from above):
img = cv2.imread(r'../images/assorted_tomatoes.jpg')
gray_img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
imgAfterLight=lightreduce(img)
imgAfterGamma=gamma_correctiom(imgAfterLight,0.8)
th2 = 255 - cv2.adaptiveThreshold(imgAfterGamma,255,cv2.ADAPTIVE_THRESH_GAUSSIAN_C,cv2.THRESH_BINARY,5,3)
median2 = cv2.medianBlur(th2,3)
where median2 is the result of shown above in edge map
and the code for connected components:
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
import cv2
import numpy as np
fname=r'../images/assorted_tomatoes.jpg'
blur_radius = 1.0
threshold = 50
img = scipy.misc.imread(fname) # gray-scale image
gray_img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
print(img.shape)
# smooth the image (to remove small objects)
imgf = ndimage.gaussian_filter(gray_img, blur_radius)
threshold = 80
# find connected components
labeled, nr_objects = ndimage.label(imgf > threshold)
where labeled is the result above
another edit:
this is the input image:
Input
The problem is that after edge detection, there are a lot of unnecessary edges in sub regions that disturbing for make smooth edge map
To me this looks like a classic problem for the watershed algorithm. It is designed for segmenting out touching objects like the tomatoes. My example is in Matlab (I'm on the wrong computer today) but it should translate to python easily. First convert to greyscale as you do and then invert the images
I=rgb2gray(img)
I2=imcomplement(I)
The image as is will over segment, so we remove minima that are too shallow. This can be done with the h-minima transform
I3=imhmin(I2,50);
You might need to play with the 50 value which is the height threshold for suppressing shallow minima. Now run the watershed algorithm and we get the following result.
L=watershed(I3);
The results are not perfect. It needs additional logic to remove some of the small regions, but it will give a reasonable estimate. The watershed and h-minima are contained in the skimage.morphology package in python.

Python: How to keep region inside canny close edge's area

I'm using canny algorithm to find the edges.
Next, I want to keep the region inside the closed curves.
My code sample is:
import cv2
import numpy as np
from matplotlib import pyplot as plt
import scipy.ndimage as nd
from skimage.morphology import watershed
from skimage.filters import sobel
img1 = cv2.imread('coins.jpg')
img = cv2.imread('coins.jpg',0)
edges= cv2.Canny(img,120,200)
markers = np.zeros_like(img)
markers[edges<50] = 0
markers[edges==255] = 1
img1[markers == 1] = [0,0,255]
img1[markers == 0] = [255,255,255]
cv2.imshow('Original', img)
cv2.imshow('Canny', img1)
#Wait for user to press a key
cv2.waitKey(0)
My output image is
I want to show the original pixels values inside the coins. Is that possible?
I suggest you use an union-find structure to get the connected components of white pixels of your img1. (You might want to find the details of this algorithm on Wikipedia : https://en.wikipedia.org/wiki/Disjoint-set_data_structure).
Once you have the connected components, my best idea is to consider the conected components that do not contain any point on the border of your picture (they should correspond to the interior of your coins) and color them in the color of img.
Sure, you may have some kind of triangles between your coins that will still be colored, but you could remove the corresponding connected components by hand.
Not really. The coin outlines are not continuous so that any kind of filling will leak.
You can repair the edges by some form of morphological processing (erosion), but this will bring the coins in contact and create unreachable regions between them.
As a fallback solution, you can try a Hough circle detector and mask inside the disks.

How to remove small connected objects using OpenCV

I use OpenCV and Python and I want to remove the small connected object from my image.
I have the following binary image as input:
The image is the result of this code:
dilation = cv2.dilate(dst,kernel,iterations = 2)
erosion = cv2.erode(dilation,kernel,iterations = 3)
I want to remove the objects highlighted in red:
How can I achieve this using OpenCV?
How about with connectedComponentsWithStats (doc):
# find all of the connected components (white blobs in your image).
# im_with_separated_blobs is an image where each detected blob has a different pixel value ranging from 1 to nb_blobs - 1.
nb_blobs, im_with_separated_blobs, stats, _ = cv2.connectedComponentsWithStats(im)
# stats (and the silenced output centroids) gives some information about the blobs. See the docs for more information.
# here, we're interested only in the size of the blobs, contained in the last column of stats.
sizes = stats[:, -1]
# the following lines result in taking out the background which is also considered a component, which I find for most applications to not be the expected output.
# you may also keep the results as they are by commenting out the following lines. You'll have to update the ranges in the for loop below.
sizes = sizes[1:]
nb_blobs -= 1
# minimum size of particles we want to keep (number of pixels).
# here, it's a fixed value, but you can set it as you want, eg the mean of the sizes or whatever.
min_size = 150
# output image with only the kept components
im_result = np.zeros_like(im_with_separated_blobs)
# for every component in the image, keep it only if it's above min_size
for blob in range(nb_blobs):
if sizes[blob] >= min_size:
# see description of im_with_separated_blobs above
im_result[im_with_separated_blobs == blob + 1] = 255
Output :
In order to remove objects automatically you need to locate them in the image.
From the image you provided I see nothing that distinguishes the 7 highlighted items from others.
You have to tell your computer how to recognize objects you don't want. If they look the same, this is not possible.
If you have multiple images where the objects always look like that you could use template matching techniques.
Also the closing operation doesn't make much sense to me.
#For isolated or unconnected blobs: Try this (you can set noise_removal_threshold to whatever you like and make it relative to the largest contour for example or a nominal value like 100 or 25).
mask = np.zeros_like(img)
for contour in contours:
area = cv2.contourArea(contour)
if area > noise_removal_threshold:
cv2.fillPoly(mask, [contour], 255)
Removing small connected components by area is called area opening. OpenCV does not have this as a function, it can be implemented as shown in other answers. But most other image processing packages will have an area opening function.
For example using scikit-image:
import skimage
import imageio.v3 as iio
img = iio.imread('cQMZm.png')[:,:,0]
out = skimage.morphology.area_opening(img, area_threshold=150, connectivity=2)
For example using DIPlib:
import diplib as dip
out = dip.AreaOpening(img, filterSize=150, connectivity=2)
PS: The DIPlib implementation is noticeably faster. Disclaimer: I'm an author of DIPlib.

Remove background of the image using opencv Python

I have two images, one with only background and the other with background + detectable object (in my case its a car). Below are the images
I am trying to remove the background such that I only have car in the resulting image. Following is the code that with which I am trying to get the desired results
import numpy as np
import cv2
original_image = cv2.imread('IMG1.jpg', cv2.IMREAD_COLOR)
gray_original = cv2.cvtColor(original_image, cv2.COLOR_BGR2GRAY)
background_image = cv2.imread('IMG2.jpg', cv2.IMREAD_COLOR)
gray_background = cv2.cvtColor(background_image, cv2.COLOR_BGR2GRAY)
foreground = np.absolute(gray_original - gray_background)
foreground[foreground > 0] = 255
cv2.imshow('Original Image', foreground)
cv2.waitKey(0)
The resulting image by subtracting the two images is
Here is the problem. The expected resulting image should be a car only.
Also, If you take a deep look in the two images, you'll see that they are not exactly same that is, the camera moved a little so background had been disturbed a little. My question is that with these two images how can I subtract the background. I do not want to use grabCut or backgroundSubtractorMOG algorithm right now because I do not know right now whats going on inside those algorithms.
What I am trying to do is to get the following resulting image
Also if possible, please guide me with a general way of doing this not only in this specific case that is, I have a background in one image and background+object in the second image. What could be the best possible way of doing this. Sorry for such a long question.
I solved your problem using the OpenCV's watershed algorithm. You can find the theory and examples of watershed here.
First I selected several points (markers) to dictate where is the object I want to keep, and where is the background. This step is manual, and can vary a lot from image to image. Also, it requires some repetition until you get the desired result. I suggest using a tool to get the pixel coordinates.
Then I created an empty integer array of zeros, with the size of the car image. And then I assigned some values (1:background, [255,192,128,64]:car_parts) to pixels at marker positions.
NOTE: When I downloaded your image I had to crop it to get the one with the car. After cropping, the image has size of 400x601. This may not be what the size of the image you have, so the markers will be off.
Afterwards I used the watershed algorithm. The 1st input is your image and 2nd input is the marker image (zero everywhere except at marker positions). The result is shown in the image below.
I set all pixels with value greater than 1 to 255 (the car), and the rest (background) to zero. Then I dilated the obtained image with a 3x3 kernel to avoid losing information on the outline of the car. Finally, I used the dilated image as a mask for the original image, using the cv2.bitwise_and() function, and the result lies in the following image:
Here is my code:
import cv2
import numpy as np
import matplotlib.pyplot as plt
# Load the image
img = cv2.imread("/path/to/image.png", 3)
# Create a blank image of zeros (same dimension as img)
# It should be grayscale (1 color channel)
marker = np.zeros_like(img[:,:,0]).astype(np.int32)
# This step is manual. The goal is to find the points
# which create the result we want. I suggest using a
# tool to get the pixel coordinates.
# Dictate the background and set the markers to 1
marker[204][95] = 1
marker[240][137] = 1
marker[245][444] = 1
marker[260][427] = 1
marker[257][378] = 1
marker[217][466] = 1
# Dictate the area of interest
# I used different values for each part of the car (for visibility)
marker[235][370] = 255 # car body
marker[135][294] = 64 # rooftop
marker[190][454] = 64 # rear light
marker[167][458] = 64 # rear wing
marker[205][103] = 128 # front bumper
# rear bumper
marker[225][456] = 128
marker[224][461] = 128
marker[216][461] = 128
# front wheel
marker[225][189] = 192
marker[240][147] = 192
# rear wheel
marker[258][409] = 192
marker[257][391] = 192
marker[254][421] = 192
# Now we have set the markers, we use the watershed
# algorithm to generate a marked image
marked = cv2.watershed(img, marker)
# Plot this one. If it does what we want, proceed;
# otherwise edit your markers and repeat
plt.imshow(marked, cmap='gray')
plt.show()
# Make the background black, and what we want to keep white
marked[marked == 1] = 0
marked[marked > 1] = 255
# Use a kernel to dilate the image, to not lose any detail on the outline
# I used a kernel of 3x3 pixels
kernel = np.ones((3,3),np.uint8)
dilation = cv2.dilate(marked.astype(np.float32), kernel, iterations = 1)
# Plot again to check whether the dilation is according to our needs
# If not, repeat by using a smaller/bigger kernel, or more/less iterations
plt.imshow(dilation, cmap='gray')
plt.show()
# Now apply the mask we created on the initial image
final_img = cv2.bitwise_and(img, img, mask=dilation.astype(np.uint8))
# cv2.imread reads the image as BGR, but matplotlib uses RGB
# BGR to RGB so we can plot the image with accurate colors
b, g, r = cv2.split(final_img)
final_img = cv2.merge([r, g, b])
# Plot the final result
plt.imshow(final_img)
plt.show()
If you have a lot of images you will probably need to create a tool to annotate the markers graphically, or even an algorithm to find markers automatically.
The problem is that you're subtracting arrays of unsigned 8 bit integers. This operation can overflow.
To demonstrate
>>> import numpy as np
>>> a = np.array([[10,10]],dtype=np.uint8)
>>> b = np.array([[11,11]],dtype=np.uint8)
>>> a - b
array([[255, 255]], dtype=uint8)
Since you're using OpenCV, the simplest way to achieve your goal is to use cv2.absdiff().
>>> cv2.absdiff(a,b)
array([[1, 1]], dtype=uint8)
I recommend using OpenCV's grabcut algorithm. You first draw a few lines on the foreground and background, and keep doing this until your foreground is sufficiently separated from the background. It is covered here: https://docs.opencv.org/trunk/d8/d83/tutorial_py_grabcut.html
as well as in this video: https://www.youtube.com/watch?v=kAwxLTDDAwU

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