python - How to completely remove the white space around a scatter plot

Question

I am trying to plot a scatterplot over an image without having any white space around it.

If I plot just the image as follows, then there is no white space:

fig = plt.imshow(im,alpha=alpha,extent=(0,1,1,0))
plt.axis('off')
fig.axes.axis('tight')
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)

but as I add a scatter plot over the image as follows:

fig = plt.scatter(sx, sy,c="gray",s=4,linewidths=.2,alpha=.5)
fig.axes.axis('tight')
fig.axes.get_xaxis().set_visible(False)
fig.axes.get_yaxis().set_visible(False)

At this point, by using the following savefig command, the white space is added around the image:

plt.savefig(im_filename,format="png",bbox_inches='tight',pad_inches=0)

Any idea on how to remove the white space definitely?

Answer 1

By switching to the mpl object-oriented style, you can plot both the image and the scatter plot on the same axes, and hence only have to set the whitespace once, by using ax.imshow and ax.scatter.

In the example below, I've used subplots_adjust to remove the whitespace around the axes, and ax.axis('tight') to set the axis limits to the data range.

import matplotlib.pyplot as plt
import numpy as np

# Load an image
im = plt.imread('stinkbug.png')

# Set the alpha
alpha = 0.5

# Some random scatterpoint data
sx = np.random.rand(100)
sy = np.random.rand(100)

# Creare your figure and axes
fig,ax = plt.subplots(1)

# Set whitespace to 0
fig.subplots_adjust(left=0,right=1,bottom=0,top=1)

# Display the image
ax.imshow(im,alpha=alpha,extent=(0,1,1,0))

# Turn off axes and set axes limits
ax.axis('tight')
ax.axis('off')

# Plot the scatter points
ax.scatter(sx, sy,c="gray",s=4,linewidths=.2,alpha=.5)

plt.show()