TypeError: only integer scalar arrays can be converted to a scalar index with 1D numpy indices array

Question

I want to write a function that randomly picks elements from a training set, based on the bin probabilities provided. I divide the set indices to 11 bins, then create custom probabilities for them.

bin_probs = [0.5, 0.3, 0.15, 0.04, 0.0025, 0.0025, 0.001, 0.001, 0.001, 0.001, 0.001]

X_train = list(range(2000000))

train_probs = bin_probs * int(len(X_train) / len(bin_probs)) # extend probabilities across bin elements
train_probs.extend([0.001]*(len(X_train) - len(train_probs))) # a small fix to match number of elements
train_probs = train_probs/np.sum(train_probs) # normalize
indices = np.random.choice(range(len(X_train)), replace=False, size=50000, p=train_probs)
out_images = X_train[indices.astype(int)] # this is where I get the error

I get the following error:

TypeError: only integer scalar arrays can be converted to a scalar index with 1D numpy indices array

I find this weird, since I already checked the array of indices that I have created. It is 1-D, it is integer, and it is scalar.

What am I missing?

Note : I tried to pass indices with astype(int). Same error.

Answer 1

I get this error whenever I use np.concatenate the wrong way:

>>> a = np.eye(2)
>>> np.concatenate(a, a)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<__array_function__ internals>", line 6, in concatenate
TypeError: only integer scalar arrays can be converted to a scalar index

The correct way is to input the two arrays as a tuple:

>>> np.concatenate((a, a))
array([[1., 0.],
       [0., 1.],
       [1., 0.],
       [0., 1.]])

Answer 2

A simple case that generates this error message:

In [8]: [1,2,3,4,5][np.array([1])]
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-8-55def8e1923d> in <module>()
----> 1 [1,2,3,4,5][np.array([1])]

TypeError: only integer scalar arrays can be converted to a scalar index

Some variations that work:

In [9]: [1,2,3,4,5][np.array(1)]     # this is a 0d array index
Out[9]: 2
In [10]: [1,2,3,4,5][np.array([1]).item()]    
Out[10]: 2
In [11]: np.array([1,2,3,4,5])[np.array([1])]
Out[11]: array([2])

Basic python list indexing is more restrictive than numpy's:

In [12]: [1,2,3,4,5][[1]]
....
TypeError: list indices must be integers or slices, not list

edit

Looking again at

indices = np.random.choice(range(len(X_train)), replace=False, size=50000, p=train_probs)

indices is a 1d array of integers - but it certainly isn't scalar. It's an array of 50000 integers. List's cannot be indexed with multiple indices at once, regardless of whether they are in a list or array.

Answer 3

Another case that could cause this error is

>>> np.ndindex(np.random.rand(60,60))
TypeError: only integer scalar arrays can be converted to a scalar index

Use the actual shape will fix it.

>>> np.ndindex(np.random.rand(60,60).shape)
<numpy.ndindex object at 0x000001B887A98880>

Answer 4

Check that you're passing the right arguments. Similar to Simon, I was passing two arrays to np.all when it only accepted one array, meaning that the second array was interpreted to be an axis.