MemoryError when running Numpy Meshgrid

Question

I have 8823 data points with x,y coordinates. I\'m trying to follow the answer on how to get a scatter dataset to be represented as a heatmap but when I go

Answer 1

in numpy 1.7.0 and newer meshgrid has the sparse keyword argument. A sparse meshgrid is setup so it broadcasts to a full meshgrid when used. This can save large amounts of memory e.g. when using the meshgrid to index arrays.

In [2]: np.meshgrid(np.arange(10), np.arange(10), sparse=True)
Out[2]: 
[array([[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]]), array([[0],
    [1],
    [2],
    [3],
    [4],
    [5],
    [6],
    [7],
    [8],
    [9]])]

Another option is to use smaller integers that are still able to represent the range:

np.meshgrid(np.arange(10).astype(np.int8), np.arange(10).astype(np.int8),
            sparse=True, copy=False)

though as of numpy 1.9 using these smaller integers for indexing will be slower as they will internally be converted back to larger integers in small (np.setbufsize sized) chunks.