Adjust contrast and save RGB images

This example shows how to adjust the contrast and intensities using scikit-image and save it as an RGB image.

When saving an RGB image to jpg, only 8 bits are supported and the image intensity needs to be rescaled to 0-255 before converting to 8 bits, otherwise, the intensities will be cropped at the value of 255.

import hyperspy.api as hs
import numpy as np
import skimage as ski

Adjust contrast

In hyperspy, color images are defined as Signal1D with the signal dimension corresponding to the color channel (red, green and blue)

# The dtype can be changed to a custom dtype, which is convenient to visualise
# the color image
s = hs.signals.Signal1D(ski.data.astronaut())
s.change_dtype("rgb8")
print(s)

<Signal2D, title: , dimensions: (|512, 512)>

Display the color image

s.plot()

Processing is usually performed on standard dtype (e.g. uint8, uint16), because most functions from scikit-image, numpy, scipy, etc. only support standard dtype. Convert from RGB to unsigned integer 16 bits

s.change_dtype("uint8")
print(s)

• 
• 

<Signal1D, title: , dimensions: (512, 512|3)>

Adjust contrast (gamma correction)

s.data = ski.exposure.adjust_gamma(s.data, gamma=0.2)

Save to jpg

Change dtype back to custom dtype rgb8

s.change_dtype("rgb8")

Save as jpg

s.save("rgb8_image.jpg", overwrite=True)

Save rgb16 image to jpg

The last part of this example shows how to save rgb16 to a jpg file

Create a signal with rgb16 dtype

s2 = hs.signals.Signal1D(ski.data.astronaut().astype("uint16") * 100)

To save a color image to jpg, the signal needs to be converted to rgb8 because jpg only support 8-bit RGB Rescale intensity to fit the unsigned integer 8 bits (2**8 = 256 intensity level)

s2.data = ski.exposure.rescale_intensity(s2.data, out_range=(0, 255))

Now that the values have been rescaled to the 0-255 range, we can convert the data type to unsigned integer 8 bit and then rgb8 to be able to save the RGB image in jpg format

s2.change_dtype("uint8")
s2.change_dtype("rgb8")
s2.save("rgb16_image_saved_as_jpg.jpg", overwrite=True)