Making image white space transparent, overlay onto imshow()

Question

I have a plot of spatial data that I display with imshow().

I need to be able to overlay the crystal lattice that produced the data. I have a png file of the lattice th

Answer 1

With out your data, I can't test this, but something like

import matplotlib.pyplot as plt
import numpy as np
import copy

my_cmap = copy.copy(plt.cm.get_cmap('gray')) # get a copy of the gray color map
my_cmap.set_bad(alpha=0) # set how the colormap handles 'bad' values
lattice = plt.imread('path')
im = plt.imshow(data[0,:,:],vmin=v_min,vmax=v_max,extent=(0,32,0,32),interpolation='nearest',cmap='jet')

lattice[lattice< thresh] = np.nan # insert 'bad' values into your lattice (the white)

im2 = plt.imshow(lattice,extent=(0,32,0,32),cmap=my_cmap)

Alternately, you can hand imshow a NxMx4 np.array of RBGA values, that way you don't have to muck with the color map

im2 = np.zeros(lattice.shape + (4,))
im2[:, :, 3] = lattice # assuming lattice is already a bool array

imshow(im2)

Answer 2

The easy way is to simply use your image as a background rather than an overlay. Other than that you will need to use PIL or Python Image Magic bindings to convert the selected colour to transparent.

Don't forget you will probably also need to resize either your plot or your image so that they match in size.

Update:

If you follow the tutorial here with your image and then plot your data over it you should get what you need, note that the tutorial uses PIL so you will need that installed as well.