How to plot 2D numpy coordinate array with corresponding RGB array?

Question

I have a 2D numpy array of coordinates (x, y) with dimensions 40000x2 that I am running through a machine learning model. I converted the prediction to an RGB numpy array with dimensions 40000x3. Each entry (row) from the RGB array corresponds to the same entry of the coordinates array.

I want to be able to quickly plot everything. Before, I tried using the scatter() function, but it took too long.

# Fragment of code I used before
# coordArray (40000x2), rgbArray (40000x3)

f, ax = plt.subplots(figsize=(7, 7))
for i in range(len(coordArray)):
    ax.scatter(coordArray[i, 0], coordArray[i, 1], marker='o', 
    c=rgbArray[i], s=1.5, alpha=1)
plt.show()

I was wondering if there was a better/quicker way to plot the data. For reference, I am also plotting my training set and test set (just not shown in the code fragment).

Michael Szczesny · Accepted Answer · 2021-01-03 02:08:53Z

1

You can create a suitable np.array and fill the coordinates with the values from rgbArray. Then plot the array with plt.imshow. Missing coordinates will be plotted as black.

import numpy as np
import matplotlib.pyplot as plt

#Example with 3 coordinates in a 2x2 array
# [0,0] -> red
# [0,1] -> green
# [1,1] -> blue
# [1,0] -> 'no information'
coord = np.array([[0,0],[0,1],[1,1]])
rgb = np.array([[1.,0.,0.],[0.,1.,0.],[0.,0.,1.]])

img = np.zeros(tuple(coord.max(0)+1)+(3,))

img[coord[:,0],coord[:,1]] = rgb
plt.imshow(img)
plt.axis('off');

Out:

If you want a scatter plot there is no need to iterate over your arrays. You can use:

plt.scatter(coord[:,0],coord[:,1], color=rgb, s=20);

Out:

edited Jan 3, 2021 at 2:08

answered Jan 3, 2021 at 1:06

Michael Szczesny

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4 Comments

optimal_transport_fan Over a year ago

Is there any way to use floats? My coordinate array mostly comprises of floating point numbers.

Michael Szczesny Over a year ago

You can just use floats in the rgb array. It's even a little bit simpler. I updated my answer to use floats in the example data.

Michael Szczesny Over a year ago

For the coordinate data I would need an example. The scatter solution without iterating could be more suitable in this case. For the 'imshow' approach we could MinMaxTransform and convert to int.

Tonechas Over a year ago

If the coordinates values are not integer numbers this approach won't work

Tonechas · Accepted Answer · 2021-01-03 02:54:55Z

1

Using vectorized code is likely to speed-up the plotting:

f, ax = plt.subplots(figsize=(7, 7))
ax.scatter(coordArray[:, 0], coordArray[:, 1], 
           marker='o', c=rgbArray/255, s=1.5, alpha=1)
plt.show()

Note that the entries of rgbArray must be in the range [0,1].

edited Jan 3, 2021 at 2:54

answered Jan 3, 2021 at 2:49

Tonechas

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