We Keep Coding

Hue output from cv2.COLOR_BGR2HSV does not correspond with calculated value

Why does cv2.COLOR_BGR2HSV give an hue output that I do not expect?
Why does is seem like cv2.COLOR_BGR2HSV is not following its documentation?
I've been doing some image analysis in Python using opencv. I want to convert RGB images to HSV. Then, using a mask I created earlier, I want to obtain the mean H, S, and V value for the masked part of the image. To do so, I'm using:
import cv2
import matplotlib.pyplot as plt
mask = #some mask I've created using thresholding
filename = '...png'
BGR_img = cv2.imread(filename)
HSV_img = cv2.cvtColor(BGR_img, cv2.COLOR_BGR2HSV)
mean_h, mean_s, mean_v, k = cv2.mean(HSV_img, mask)
I get the following output:
mean_h = 144.36
mean_s = 154.34
mean_v = 52.56
I want to check whether this output makes sense, so I have the following idea: obtain the mean R, mean G and mean B values for the same masked image and calculate 'by hand' what the corresponding mean H, mean S, mean V values should be. For this calculation, I follow opencv's documentation on color conversions (https://docs.opencv.org/2.4/modules/imgproc/doc/miscellaneous_transformations.html?highlight=cvtcolor#cvtcolor). My assumption is that the mean HSV values I calculate using the documentation, should correspond with my output from cv2.COLOR_BGR2HSV (= values above). After all, the function cv2.COLOR_BGR2HSV does what is stated in the documentation! My assumptions seems to be incorrect..
I used a similar method as above to obtain mean_r, mean_g, mean_b and checked with ImageJ -> analyse -> histogram if these values made sense (they did!). I got:
mean_r = 52.27
mean_g = 21.30
mean_b = 30.05
Then from the documentation I follow these steps (I work with 8-bit images):
To get:
mean_h_calculated = 171.58
mean_s_calculated = 151.13
mean_v_calculated = 52.3
Obviously mean_h does not equal mean_h_calculated. In other words, the mean hue I get from using cv2.COLOR_BGR2HSV does not correspond with the value I calculate myself when using the documentation. (for s and v I can accept that there is a small difference) I expect the hue to be around 171 because the masked part of the image that I'm analysing is red.
Why does cv2.COLOR_BGR2HSV give an hue output that I do not expect?
Why does is seem like cv2.COLOR_BGR2HSV is not following its documentation?
I would appreciate any help! Thank you!
p.s. I think it has nothing to do with the scaling of hue (0-180 instead of 0-255).

Python: Normalize image exposure

I'm working on a project to measure and visualize image similarity. The images in my dataset come from photographs of images in books, some of which have very high or low exposure rates. For example, the images below come from two different books; the one on the top is an over-exposed reprint of the one on the bottom, wherein the exposure looks good:
I'd like to normalize each image's exposure in Python. I thought I could do so with the following naive approach, which attempts to center each pixel value between 0 and 255:
from scipy.ndimage import imread
import sys
def normalize(img):
'''
Normalize the exposure of an image.
#args:
{numpy.ndarray} img: an array of image pixels with shape:
(height, width)
#returns:
{numpy.ndarray} an image with shape of `img` wherein
all values are normalized such that the min=0 and max=255
'''
_min = img.min()
_max = img.max()
return img - _min * 255 / (_max - _min)
img = imread(sys.argv[1])
normalized = normalize(img)
Only after running this did I realize that this normalization will only help images whose lightest value is less than 255 or whose darkest value is greater than 0.
Is there a straightforward way to normalize the exposure of an image such as the top image above? I'd be grateful for any thoughts others can offer on this question.

Histogram equalisation works surprisingly well for this kind of thing. It's usually better for photographic images, but it's helpful even on line art, as long as there are some non-black/white pixels.
It works well for colour images too: split the bands up, equalize each one separately, and recombine.
I tried on your sample image:
Using libvips:
$ vips hist_equal sample.jpg x.jpg
Or from Python with pyvips:
x = pyvips.Image.new_from_file("sample.jpg")
x = x.hist_equal()
x.write_to_file("x.jpg")

It's very hard to say if it will work for you without seeing a larger sample of your images, but you may find an "auto-gamma" useful. There is one built into ImageMagick and the description - so that you can calculate it yourself - is:
Automagically adjust gamma level of image.
This calculates the mean values of an image, then applies a calculated
-gamma adjustment so that the mean color in the image will get a value of 50%.
This means that any solid 'gray' image becomes 50% gray.
This works well for real-life images with little or no extreme dark
and light areas, but tend to fail for images with large amounts of
bright sky or dark shadows. It also does not work well for diagrams or
cartoon like images.
You can try it out yourself on the command line very simply before you go and spend a lot of time coding something that may not work:
convert Tribunal.jpg -auto-gamma result.png
You can do -auto-level as per your own code beforehand, and a thousand other things too:
convert Tribunal.jpg -auto-level -auto-gamma result.png

I ended up using a numpy implementation of the histogram normalization method #user894763 pointed out. Just save the below as normalize.py then you can call:
python normalize.py cats.jpg
Script:
import numpy as np
from scipy.misc import imsave
from scipy.ndimage import imread
import sys
def get_histogram(img):
'''
calculate the normalized histogram of an image
'''
height, width = img.shape
hist = [0.0] * 256
for i in range(height):
for j in range(width):
hist[img[i, j]]+=1
return np.array(hist)/(height*width)
def get_cumulative_sums(hist):
'''
find the cumulative sum of a numpy array
'''
return [sum(hist[:i+1]) for i in range(len(hist))]
def normalize_histogram(img):
# calculate the image histogram
hist = get_histogram(img)
# get the cumulative distribution function
cdf = np.array(get_cumulative_sums(hist))
# determine the normalization values for each unit of the cdf
sk = np.uint8(255 * cdf)
# normalize the normalization values
height, width = img.shape
Y = np.zeros_like(img)
for i in range(0, height):
for j in range(0, width):
Y[i, j] = sk[img[i, j]]
# optionally, get the new histogram for comparison
new_hist = get_histogram(Y)
# return the transformed image
return Y
img = imread(sys.argv[1])
normalized = normalize_histogram(img)
imsave(sys.argv[1] + '-normalized.jpg', normalized)
Output:

Binarize image data

I have 10 greyscale brain MRI scans from BrainWeb. They are stored as a 4d numpy array, brains, with shape (10, 181, 217, 181). Each of the 10 brains is made up of 181 slices along the z-plane (going through the top of the head to the neck) where each slice is 181 pixels by 217 pixels in the x (ear to ear) and y (eyes to back of head) planes respectively.
All of the brains are type dtype('float64'). The maximum pixel intensity across all brains is ~1328 and the minimum is ~0. For example, for the first brain, I calculate this by brains[0].max() giving 1328.338086605072 and brains[0].min() giving 0.0003886114541273855. Below is a plot of a slice of a brain[0]:
I want to binarize all these brain images by rescaling the pixel intensities from [0, 1328] to {0, 1}. Is my method correct?
I do this by first normalising the pixel intensities to [0, 1]:
normalized_brains = brains/1328
And then by using the binomial distribution to binarize each pixel:
binarized_brains = np.random.binomial(1, (normalized_brains))
The plotted result looks correct:
A 0 pixel intensity represents black (background) and 1 pixel intensity represents white (brain).
I experimented by implementing another method to normalise an image from this post but it gave me just a black image. This is because np.finfo(np.float64) is 1.7976931348623157e+308, so the normalization step
normalized_brains = brains/1.7976931348623157e+308
just returned an array of zeros which in the binarizition step also led to an array of zeros.
Am I binarising my images using a correct method?

Your method of converting the image to a binary image basically amounts to random dithering, which is a poor method of creating the illusion of grey values on a binary medium. Old-fashioned print is a binary medium, they have fine-tuned the methods to represent grey-value photographs in print over centuries. This process is called halftoning, and is shaped in part by properties of ink on paper, that we do not have to deal with in binary images.
So what methods have people come up with outside of print? Ordered dithering (mostly Bayer matrix), and error diffusion dithering. Read more about dithering on Wikipedia. I wrote a blog post showing how to implement all of these methods in MATLAB some years ago.
I would recommend you use error diffusion dithering for your particular application. Here is some code in MATLAB (taken from my blog post liked above) for the Floyd-Steinberg algorithm, I hope that you can translate this to Python:
img = imread('https://i.stack.imgur.com/d5E9i.png');
img = img(:,:,1);
out = double(img);
sz = size(out);
for ii=1:sz(1)
for jj=1:sz(2)
old = out(ii,jj);
%new = 255*(old >= 128); % Original Floyd-Steinberg
new = 255*(old >= 128+(rand-0.5)*100); % Simple improvement
out(ii,jj) = new;
err = new-old;
if jj<sz(2)
% right
out(ii ,jj+1) = out(ii ,jj+1)-err*(7/16);
end
if ii<sz(1)
if jj<sz(2)
% right-down
out(ii+1,jj+1) = out(ii+1,jj+1)-err*(1/16);
end
% down
out(ii+1,jj ) = out(ii+1,jj )-err*(5/16);
if jj>1
% left-down
out(ii+1,jj-1) = out(ii+1,jj-1)-err*(3/16);
end
end
end
end
imshow(out)
Resampling the image before applying the dithering greatly improves the results:
img = imresize(img,4);
% (repeat code above)
imshow(out)
NOTE that the above process expects the input to be in the range [0,255]. It is easy to adapt to a different range, say [0,1328] or [0,1], but it is also easy to scale your images to the [0,255] range.

Have you tried a threshold on the image?
This is a common way to binarize images, rather than trying to apply a random binomial distribution. You could try something like:
binarized_brains = (brains > threshold_value).astype(int)
which returns an array of 0s and 1s according to whether the image value was less than or greater than your chosen threshold value.
You will have to experiment with the threshold value to find the best one for your images, but it does not need to be normalized first.
If this doesn't work well, you can also experiment with the thresholding options available in the skimage filters package.

IT is easy in OpenCV. as mentioned a very common way is defining a threshold, But your result looks like you are allocating random values to your intensities instead of thresholding it.
import cv2
im = cv2.imread('brain.png', cv2.CV_LOAD_IMAGE_GRAYSCALE)
(th, brain_bw) = cv2.threshold(imy, 128, 255, cv2.THRESH_BINARY | cv2.THRESH_OTSU)
th = (DEFINE HERE)
im_bin = cv2.threshold(im, th, 255, cv
cv2.imwrite('binBrain.png', brain_bw)
brain
binBrain

OpenCV - Managing thresholds in image processing with python

I am new to image processing and I am processing the following image and applying threshold to identify edges with the following code
import cv2
import numpy as np
img = cv2.imread("box.jpg")
img_gray = cv2.cvtColor(img,cv2.COLOR_RGB2GRAY)
noise_removal = cv2.bilateralFilter(img_gray,9,75,75)
ret,thresh_image = cv2.threshold(noise_removal,0,255,cv2.THRESH_OTSU)
On the left is the original image. In the middle is the gray image calculated by img_gray in the code. On the right is the threshold image calculated by thresh_imgage.
My question is from image 1 and 2 we can see that there is a significant change in the gradient at the corners but in the threshold image it is also including shadow as the part of box object.
I have run the code several times by changing threshold values but did not succeed to get only the box. What am I doing wrong ? Can someone help in this ? Thanks.

You should have considered trying adaptive threshold
adp_th = cv2.adaptiveThreshold(img,255,cv2.ADAPTIVE_THRESH_MEAN_C,cv2.THRESH_BINARY, 5, 1.8)
This is what I got:
Now playing with the morphological operations mentioned on THIS PAGE you can obtain your desired object.

I just came across another solution regarding selection of optimal thresholds for edge detection. My previous answer was about adaptive threshold of which you know very well.
By optimal I mean choosing a two values (lower and upper thresholds) based on the median value of the gray scale image. The following code shows you how its done:
v = np.median(gray_img)
sigma = 0.33
#---- apply optimal Canny edge detection using the computed median----
lower_thresh = int(max(0, (1.0 - sigma) * v))
upper_thresh = int(min(255, (1.0 + sigma) * v))
edge_img = cv2.Canny(gray_img, lower_thresh, upper_thresh)
cv2.imshow('Edge_of_box',edge_img)
The sigma value of 0.33 is the most optimal value in the field of data science.
Illustration: If you observe a Gaussian curve in statistics, values between 0.33 from both sides of the curve are considered in the distribution. Any value outside these points are assumed to be outliers. Since images are considered to be data, this concept is assumed here as well.
Have a look at this:
Now the second box which you so frequently post:
How can you improve this?
I always wanted to try out the following. Give it a try and do let me know:
First try replacing median value with mean and observe the
results.
Change the sigma value and observe how edge detection changes.
Try performing the above mentioned technique for a small patch of the image. Divide the image into small patches and work your way through. (My way of saying 'Localized edge detection')
There might be better ways to detect out there which I have not come across yet. But this is a great and fun way to start.

Python - matplotlib - imshow - How to influence displayed value of unzoomed image

I need to search outliers in more or less homogeneous images representing some physical array. The images have a resolution which is much higher than the screen resolution. Thus every pixel on screen originates from a block of image pixels. Is there the possibility to customize the algorithm which calculates the displayed value for such a block? Especially the possibility to either use the lowest or the highest value would be helpful.
Thanks in advance

Scipy provides several such filters. To get a new image (new) whose pixels are the maximum/minimum over a w*w block of an original image (img), you can use:
new = scipy.ndimage.filters.maximum_filter(img, w)
new = scipy.ndimage.filters.minimum_filter(img, w)
scipy.ndimage.filters has several other filters available.
If the standard filters don't fit your requirements, you can roll your own. To get you started here is an example that shows how to get the minimum in each block in the image. This function reduces the size of the full image (img) by a factor of w in each direction. It returns a smaller image (new) in which each pixel is the minimum pixel in a w*w block of pixels from the original image. The function assumes the image is in a numpy array:
import numpy as np
def condense(img, w):
new = np.zeros((img.shape[0]/w, img.shape[1]/w))
for i in range(0, img.shape[1]//w):
col1 = i * w
new[:, i] = img[:, col1:col1+w].reshape(-1, w*w).min(1)
return new
If you wanted the maximum, replace min with max.
For the condense function to work well, the size of the full image must be a multiple of w in each direction. The handling of non-square blocks or images that don't divide exactly is left as an exercise for the reader.