Python numpy ValueError: setting an array element with a sequence

I can reproduce the error message with this code:

import numpy as np
def rotate_by_90_deg(im):
    new_mat=np.zeros((im.shape[1],im.shape[0]),  dtype=np.uint8)
    n = im.shape[0]
    for x in  range(im.shape[0]):
        for y in range(im.shape[1]):
            new_mat[y,n-1-x]=im[x,y]
    return new_mat

im = np.arange(27).reshape(3,3,3)
rotate_by_90_deg(im)

The problem here is that im is 3-dimensional, not 2-dimensional. That might happen if your image is in RGB format, for example. So im[x,y] is an array of shape (3,). new_mat[y, n-1-x] expects a np.uint8 value, but instead is getting assigned to an array.

To fix rotate_by_90_deg, make new_mat have the same number of axes as im:

import numpy as np
import matplotlib.pyplot as plt
np.random.seed(1)

def rotate_by_90_deg(im):
    H, W, V = im.shape[0], im.shape[1], im.shape[2:]
    new_mat = np.empty((W, H)+V, dtype=im.dtype)
    n = im.shape[0]
    for x in  range(im.shape[0]):
        for y in range(im.shape[1]):
            new_mat[y,n-1-x]=im[x,y]
    return new_mat

im = np.random.random((3,3,3))
arr = rotate_by_90_deg(im)
fig, ax = plt.subplots(ncols=2)
ax[0].imshow(10*im, interpolation='nearest')
ax[0].set_title('orig')
ax[1].imshow(10*arr, interpolation='nearest')
ax[1].set_title('rot90')
plt.show()

Or, you could use np.rot90:

import numpy as np
import matplotlib.pyplot as plt
np.random.seed(1)
im = np.random.random((3,3,3))
arr = np.rot90(im, 3)
fig, ax = plt.subplots(ncols=2)
ax[0].imshow(10*im, interpolation='nearest')
ax[0].set_title('orig')
ax[1].imshow(10*arr, interpolation='nearest')
ax[1].set_title('rot90')
plt.show()