Figures overlapping when plotting using Matplotlib

Question

I have a plot with multiple images. There are 20 rows and 3 columns. In each row the 1st column should be the original image, the 2nd column should be the mask and the 3rd column should be segmentation obtained using a neural network.

I tried using the below code. 2 rows can be plotted correctly. From 3rd row images overlap the 1st row.

f = plt.figure()
for j in range(3):
    pred_y = y_pred[j]
    pred_y = pred_y.reshape(256, 256)
    pred_y = (pred_y > 0.1).astype(np.uint8)
    f.add_subplot(j + 1, 3, 1 )
    plt.imshow(X_test[j, :, :])

    f.add_subplot(j + 1, 3, 2)
    plt.imshow(y_test[j])
    
    f.add_subplot(j + 1, 3, 3)
    plt.imshow(pred_y)
plt.show()

The obtained output is,

@mozway. I'd argue that there's sufficient information here. An MCVE would use np.ones((256, 256), 'uint8') or a random array instead of the images. — Mad Physicist
– Mad Physicist, Commented Feb 9, 2022 at 9:20
You might want to refer to https://matplotlib.org/stable/gallery/subplots_axes_and_figures/demo_constrained_layout.html#sphx-glr-gallery-subplots-axes-and-figures-demo-constrained-layout-py. — r-beginners
– r-beginners, Commented Feb 9, 2022 at 9:22

Mad Physicist · Accepted Answer · 2022-02-09 09:29:58Z

1

The arguments to Figure.add_subplot are num_rows, num_cols, n, not row, num_rows, col. You are therefore making the top row of plots in a 1x3, 2x3, 3x3 arrangement. Make your calls to add_subplot like this:

f.add_subplot(20, 3, 3 * j + 1)
f.add_subplot(20, 3, 3 * j + 2)
f.add_subplot(20, 3, 3 * j + 1)

A better way to generate your axes might be plt.subplots, as suggested in the demo:

fig, ax = plt.subplots(20, 3, constrained_layout=True)
for i in range(20):
    ax[i, 0].imshow(X_test[i])
    ax[i, 1].imshow(y_test[j])
    ax[i, 2].imshow((pred_y[j].reshape(256, 256) > 0.1).astype(np.uint8))

edited Feb 9, 2022 at 9:29

answered Feb 9, 2022 at 9:19

Mad Physicist

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2 Comments

Aleena Over a year ago

It really helped. Thank you. Bu the size is very small. Is there any way to increase that. Corresponding output can be seen in the link drive.google.com/file/d/1nHrP3oHp0HDu-bwlJ05kJ6MdnYh3gRO2/…

Mad Physicist Over a year ago

@Aleena. Don't display 20 rows all at once. Maybe call it off at 3 per figure or a separate figure for each image

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