2

I am plotting an image with matplotlib, by far the best interpolation parameter for imshow in my case is interpolation='None' but if I also give an alpha parameter, when saving the figure, the alpha is not kept.

Minimal example:

import matplotlib.pyplot as plt
import numpy as np

arr = np.abs(np.sin(np.linspace(0, 2*np.pi)))
x,y = np.meshgrid(arr,arr)
arr = x*y
plt.figure()
plt.imshow(arr,alpha=arr,interpolation='None')
plt.savefig("fig1.pdf")

expected result:

enter image description here

what I get:

enter image description here

I only experience this issue for this particular interpolation setting.

matplotlib version: 3.4.3

mapf
  • 1,906
  • 1
  • 14
  • 40
matmoa
  • 21
  • 3

2 Answers2

2

@mapf suggestion to rasterize is good, but you can just rasterize the image, and not the whole axes; that keeps the axes labels etc as vectors.

import matplotlib.pyplot as plt
import numpy as np

arr = np.abs(np.sin(np.linspace(0, 2*np.pi)))
x,y = np.meshgrid(arr, arr)
arr = x*y
fig, ax = plt.subplots()
ax.imshow(arr, alpha=arr, interpolation='none', rasterized=True)
fig.savefig("fig1.pdf")

enter image description here

If you really want the image to be vectorized, then save as pcolormesh:

fig, ax = plt.subplots()
ax.pcolormesh(arr, alpha=arr)
fig.savefig("fig2.pdf")

enter image description here

If you want imshow's vertical orientation and aspect ratio:

ax.flipud()
ax.set_aspect(1)
Jody Klymak
  • 4,979
  • 2
  • 15
  • 31
1

Even though pdf supports transparency (unlike eps), if you use interpolation='None', you need to force a rasterized (bitmap) drawing, by using ax.set_rasterized(True):

import matplotlib.pyplot as plt
import numpy as np

arr = np.abs(np.sin(np.linspace(0, 2*np.pi)))
x,y = np.meshgrid(arr, arr)
arr = x*y

fig, ax = plt.subplots()

ax.imshow(arr, alpha=arr, interpolation='None')
ax.set_rasterized(True)

fig.savefig("fig1.pdf")

Note that by doing this, you are no longer saving a vector graphic (and unfortunately loose all the benefits that come with it). Instead, you essentially generate a png that is then incorporated into a pdf. Thus to avoid pixelation, you will probably need to up the dpi.

Nevertheless, the easiest solution would probably be to just drop interpolation='None', unless you really need it.

Since you said that interpolation='None' works best for your project, but for every other backend except Agg, ps, pdf and svg the interpolation defaults to 'nearest', what likely actually works best for your project is interpolation='nearest'. So I would recommend to try that instead.

mapf
  • 1,906
  • 1
  • 14
  • 40
  • Thank you for your solution, it does indeed work but I attach a lot of importance to the output still being vectorially drawn ( otherwise saving as a high quality raster was always a solution). I think I will implement my own alpha method to modify the image and drop the `alpha` parameter in imshow. – matmoa Nov 10 '21 at 14:44
  • @matmoa Well the problem lies with `interpolation='None'`. A much simpler way would just be to drop that statement. – mapf Nov 10 '21 at 15:10
  • @matmoa see my new edit about trying `interpolation='nearest'`. – mapf Nov 10 '21 at 15:17