Histogram equalization of grayscale images with NumPy

Question

How to do histogram equalization for multiple grayscaled images stored in a NumPy array easily?

I have the 96×96 pixel NumPy data in this 4D format:

(1800, 1, 96,96)

Asked By: pbu

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Source

Answer 1

Moose’s comment which points to this blog entry does the job quite nicely.

For completeness, I give an example here using nicer variable names and a looped execution on 1000 96×96 images which are in a 4D array as in the question. It is fast (1-2 seconds on my computer) and only needs NumPy.

import numpy as np

def image_histogram_equalization(image, number_bins=256):
    # from http://www.janeriksolem.net/histogram-equalization-with-python-and.html

    # get image histogram
    image_histogram, bins = np.histogram(image.flatten(), number_bins, density=True)
    cdf = image_histogram.cumsum() # cumulative distribution function
    cdf = (number_bins-1) * cdf / cdf[-1] # normalize

    # use linear interpolation of cdf to find new pixel values
    image_equalized = np.interp(image.flatten(), bins[:-1], cdf)

    return image_equalized.reshape(image.shape), cdf

if __name__ == '__main__':

    # generate some test data with shape 1000, 1, 96, 96
    data = np.random.rand(1000, 1, 96, 96)

    # loop over them
    data_equalized = np.zeros(data.shape)
    for i in range(data.shape[0]):
        image = data[i, 0, :, :]
        data_equalized[i, 0, :, :] = image_histogram_equalization(image)[0]

Answered By: Trilarion

Answer 2

Very fast and easy way is to use the cumulative distribution function provided by the skimage module. Basically what you do mathematically to proof it.

from skimage import exposure
import numpy as np
def histogram_equalize(img):
    img = rgb2gray(img)
    img_cdf, bin_centers = exposure.cumulative_distribution(img)
    return np.interp(img, bin_centers, img_cdf)

Answered By: Dodo

Answer 3

As of today janeriksolem‘s url is broken.

I found however this gist that links the same page and claims to perform histogram equalization without computing the histogram.

The code is:

img_eq = np.sort(img.ravel()).searchsorted(img)

Answered By: Diego Ferri

Answer 4

Here’s an alternate implementation for a single channel image that is fast. See skimage.exposure.histogram for reference. Using timeit, ‘image_histogram_equalization’ in Trilarion’s answer has a mean execution time was 0.3696 seconds, while this function has a mean execution time of 0.0534 seconds. However this implementation also relies on skimage.

import numpy as np
from skimage import exposure

def hist_eq(image):
    hist, bins = exposure.histogram(image, nbins=256, normalize=False)
    # append any remaining 0 values to the histogram
    hist = np.hstack((hist, np.zeros((255 - bins[-1])))) 
    cdf = 255*(hist/hist.sum()).cumsum()
    equalized = cdf[image].astype(np.uint8)

    return equalized

Answered By: Isaac Berrios

Histogram equalization of grayscale images with NumPy

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