matplotlib markers / mask on image pixels

Question

So I have an image and I have a pixel mask for that image, where the mask is the same size as the image and contains values of 0 and 1, where if it is 0 I don't want to modify the image, and if it is 1 I want to add a transparent color over that pixel of the image.

Basically I want to highlight certain segments of the image but still see what is underneath.

Now I have searched high and low but haven't found a simple way to do this. I used np.where with the mask to get the pixel locations of the 1's to use with the plot functions. I first tried scatter plots with a small marker size and no edge color (small scatter plot markers in matplotlib are always black), but the markers are not one image pixel in size, they seem to be an absolute size and so depending on the size of the figure the transparency is affected and weird patterns are created from the overlapping markers.

Just the regular pyplot plot function created the exact look I desired (where the coloring was smooth and invariant to figure size) but it also colored horizontal connections between disjoint segments in the mask (since it is drawing lines I guess), so I couldn't use that.

What worked the best was patches, which I came across in this question: (How to set a fixed/static size of circle marker on a scatter plot?). I found that rectangular patches with width and height of 1 gave me the exact desired effect, where I could put a transparent color over certain pixels of the image. However this proved to produce a ton (tens of thousands) of rectangles for certain images, and so it was quite slow. Even when using a PatchCollection instead of calling addPatch every time it was still slow.

Now I can probably just join adjacent rectangles to reduce the number of things needing to be drawn, but I was just wondering if there was an easier way to do this?

Thanks.

Answer 1

You can do a semitransparent overlay either using masked arrays or by setting the alpha values in an RGBA image. Here are both worked through (using the example of three semitransparent red squares placed over a circular pattern), and they give similar images (so I'll only show one):

from pylab import *
from numpy import ma

x = y = linspace(-6, 6, 100)
X, Y = meshgrid(x, y)

z3 = X*X + Y*Y  # circular pattern

# first, do this with a masked array
figure()
# z4 = 3 diagonal square
# zm = a uniform image (ones), with a mask of squares (~z4)
z4 =  np.repeat(np.repeat(eye(3, dtype=bool), 40, axis=0), 40, axis=1)
zm = ma.masked_where(~z4, ones((120,120)))
imshow(z3, cmap=cm.jet)
imshow(zm, cmap=cm.bwr, alpha=.3, vmin=0, vmax=1) #cm.bwr is an easy way to get red

# do this by changing alpha for each pixel
figure()
z5 = zeros((120, 120, 4), dtype=float)
z5[..., 0] = 1
z5[..., 3] = .4*z4.astype(float)
imshow(z3, cmap=cm.jet)
imshow(z5)

show()

I think both approaches can produce the same results for all cases, but:
1. the masked arrays can be a more direct approach if the mask or composition becomes complicated, and masking gives you more flexibility in drawing your overlay image since, for example, you can use colormaps rather than specifying the full RGBA for every pixel, but,
2. the masked array approach doesn't give full pixel-by-pixel control over the alpha value like RGBA does.

z1 = sin(X*Y)
z1 = cos(2*X)
z2 = cos(5*(X+Y))

zm = ma.masked_where( (z2<.5) & (Y>0), z1)

figure()
imshow(z3)
imshow(zm, cmap=cm.gray, alpha=.4, vmin=-2, vmax=2)
show()

It's a bit crazy, but here's what's going on: The primary image is a circular pattern that goes from blue to red (z3). Then there are vertical bars that faintly shade this (z1) but only in half of the figure and in narrow alternate diagonal bands on the other half (due to the mask). Here's a more complicated image using masked arrays:

Answer 2

Just to add on to what tom10 has posted, the masked arrays do work great with colormaps, but I also wrote a small function in the meantime that should work with any RGB color tuple.

def overlayImage(im, mask, col, alpha):
    maskRGB = np.tile(mask[..., np.newaxis], 3)
    untocuhed = (maskRGB == False) * im
    overlayComponent = alpha * np.array(col) * maskRGB
    origImageComponent = (1 - alpha) * maskRGB * im
    return untocuhed + overlayComponent + origImageComponent

im is the rgb image

mask is a boolean mask of the image, such that mask.shape + (3,) = im.shape

col is just the 3-tuple rgb value you want to mask the image with

alpha is just the alpha value / transparency for the mask

Answer 3

I also needed a clear contour on my areas. Thus, you can easily add a contour plot on top: e.g., create a dummy numpy array and set a different value in each area of interest. Here's an example build on top of tom10's answer with a different condition:

x = y = linspace(-6, 6, 100)
X, Y = meshgrid(x, y)

z3 = X*X + Y*Y  # circular pattern

# first, do this with a masked array
figure()
imshow(z3, cmap=cm.jet, extent = (-6,6,-6,6));
zm = ma.masked_where((z3>=0.7) & (z3<=1.5), ones(np.shape(z3)));
imshow(zm, cmap=cm.bwr, alpha=.4, vmin=0, vmax=1, extent = (-6,6,-6,6)) #cm.bwr is an easy way to get red
# Build dummy array of 1s and 0s (you can play with different values to obtain different contours for different regions):
temp_vector = ones(np.shape(z3));
temp_vector[(z3>=0.7) & (z3<=1.5)] = 0.0;
temp_vector[(z3>8.2)] = 2.0; # etc.
# Create contour. I found only one contour necessary:
contour(X, Y, temp_vector, 1, colors=['r','g']);


show()

Which yields: