Indexing with Masked Arrays in numpy

Question

I have a bit of code that attempts to find the contents of an array at indices specified by another, that may specify indices that are out of range of the former array.

input = np.arange(0, 5)
indices = np.array([0, 1, 2, 99])

What I want to do is this: print input[indices] and get [0 1 2]

But this yields an exception (as expected):

IndexError: index 99 out of bounds 0<=index<5

So I thought I could use masked arrays to hide the out of bounds indices:

indices = np.ma.masked_greater_equal(indices, 5)

But still:

>print input[indices]
IndexError: index 99 out of bounds 0<=index<5

Even though:

>np.max(indices)
2

So I'm having to fill the masked array first, which is annoying, since I don't know what fill value I could use to not select any indices for those that are out of range:

print input[np.ma.filled(indices, 0)]

[0 1 2 0]

So my question is: how can you use numpy efficiently to select indices safely from an array without overstepping the bounds of the input array?

Answer 1

Without using masked arrays, you could remove the indices greater or equal to 5 like this:

print input[indices[indices<5]]

Edit: note that if you also wanted to discard negative indices, you could write:

print input[indices[(0 <= indices) & (indices < 5)]]

Answer 2

It is a VERY BAD idea to index with masked arrays. There was a (very short) time with using MaskedArrays for indexing would have thrown an exception, but it was a bit too harsh...

In your test, you're filtering indices to find the entries matching a condition. What should you do with the missing entries of your MaskedArray ? Is the condition False ? True ? Should you use a default ? It's up to you, the user, to decide what to do.

Using indices.filled(0) means that when an item of indices is masked (as in, undefined), you want to take the first index (0) as default. Probably not what you wanted.

Here, I would have simply used input[indices.compressed()] : the compressed method flattens your MaskedArray, keeping only the unmasked entries.

But as you realized, you probably didn't need MaskedArrays in the first place