Matplotlib Image Transparency

Introduction

This lab will show you how to blend transparency with color in 2D images using Matplotlib. The goal is to highlight certain parts of data with imshow.

VM Tips

After the VM startup is done, click the top left corner to switch to the Notebook tab to access Jupyter Notebook for practice.

Sometimes, you may need to wait a few seconds for Jupyter Notebook to finish loading. The validation of operations cannot be automated because of limitations in Jupyter Notebook.

If you face issues during learning, feel free to ask Labby. Provide feedback after the session, and we will promptly resolve the problem for you.

Generate Data

We will start by generating two 2D blobs in a 2D grid. One blob will be positive, and the other negative.

import matplotlib.pyplot as plt
import numpy as np
from matplotlib.colors import Normalize

def normal_pdf(x, mean, var):
    return np.exp(-(x - mean)**2 / (2*var))

## Generate the space in which the blobs will live
xmin, xmax, ymin, ymax = (0, 100, 0, 100)
n_bins = 100
xx = np.linspace(xmin, xmax, n_bins)
yy = np.linspace(ymin, ymax, n_bins)

## Generate the blobs. The range of the values is roughly -.0002 to .0002
means_high = [20, 50]
means_low = [50, 60]
var = [150, 200]

gauss_x_high = normal_pdf(xx, means_high[0], var[0])
gauss_y_high = normal_pdf(yy, means_high[1], var[0])

gauss_x_low = normal_pdf(xx, means_low[0], var[1])
gauss_y_low = normal_pdf(yy, means_low[1], var[1])

weights = (np.outer(gauss_y_high, gauss_x_high)
           - np.outer(gauss_y_low, gauss_x_low))

## We'll also create a grey background into which the pixels will fade
greys = np.full((*weights.shape, 3), 70, dtype=np.uint8)

Plot the Blobs

Next, we will plot these blobs using imshow without transparency.

vmax = np.abs(weights).max()
imshow_kwargs = {
    'vmax': vmax,
    'vmin': -vmax,
    'cmap': 'RdYlBu',
    'extent': (xmin, xmax, ymin, ymax),
}

fig, ax = plt.subplots()
ax.imshow(greys)
ax.imshow(weights, **imshow_kwargs)
ax.set_axis_off()
plt.show()

Blend in Transparency

The simplest way to include transparency when plotting data with imshow is to pass an array matching the shape of the data to the alpha argument.

## Create an alpha channel of linearly increasing values moving to the right.
alphas = np.ones(weights.shape)
alphas[:, 30:] = np.linspace(1, 0, 70)

## Create the figure and image
fig, ax = plt.subplots()
ax.imshow(greys)
ax.imshow(weights, alpha=alphas, **imshow_kwargs)
ax.set_axis_off()
plt.show()

Use Transparency to Highlight Values

Finally, we'll recreate the same plot, but this time we'll use transparency to highlight the extreme values in the data. This is often used to highlight data points with smaller p-values. We'll also add in contour lines to highlight the image values.

## Create an alpha channel based on weight values
alphas = Normalize(0, .3, clip=True)(np.abs(weights))
alphas = np.clip(alphas, .4, 1)  ## alpha value clipped at the bottom at .4

## Create the figure and image
fig, ax = plt.subplots()
ax.imshow(greys)
ax.imshow(weights, alpha=alphas, **imshow_kwargs)

## Add contour lines to further highlight different levels.
ax.contour(weights[::-1], levels=[-.1, .1], colors='k', linestyles='-')
ax.set_axis_off()
plt.show()

ax.contour(weights[::-1], levels=[-.0001, .0001], colors='k', linestyles='-')
ax.set_axis_off()
plt.show()

Summary

In this lab, we learned how to blend transparency with color in 2D images using Matplotlib. We also learned how to highlight certain parts of data with imshow.