Pythonic way to create a numpy array of coordinates

Question

I'm trying to create a numpy array of coordinates. Up until now, I've been just using x_coords, y_coords = numpy.indices((shape)). Now, however, I want to combine x_coords and y_coords into one array, such that x_coords = thisArray[:,:,0] and y_coords = thisArray[:,:,1] In this case, thisArray is a two-dimensional array. Is there a simple or pythonic way to do this?

I originally thought about using numpy.outer, but that doesn't quite give me what I need. A possible idea is just using concatenation of the indices array along the (2nd?) axis, but that doesn't seem like a very elegant solution. (it may be the cleanest one here though).

Thanks!

Jaime · Accepted Answer · 2013-06-22 02:29:57Z

2

What np.indices returns is already an array, but x_coords = thisArray[0, :, :] and y_coords = thisArray[1, :, :]. Unless you have very strict requirements for your array of coordinates (namely that it be contiguous), you can take a view of that array with the first axis rolled to the end:

thisArray = numpy.rollaxis(numpy.indices(shape), 0, len(shape)+1)

answered Jun 22, 2013 at 2:29

Jaime

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4 Comments

James Over a year ago

Hm, that seems to work -- what do you mean though by the condition that it be contiguous. (Are you talking about its location in memory?)

Jaime Over a year ago

When you roll the axis, the memory layout of the data is not changed, only the strides of the array. In memory, all the x coordinates will be together at the beginning of the memory section, followed by all the y coordinates. If you created your array directly with the shape you are after, x and y coordinates would be alternating in memory. For some fancy stuff, the actual memory layout may slow certain computations, or require a copy of the array, which is slow. For instance, you cannot feed a non-contiguous array to np.frombuffer. But for most applications it is not an issue at all.

James Over a year ago

Hm okay, thanks. One more question then. Suppose I wanted to flatten the 2nd and third axis. (Because I don't really care what order they are in. I pretty much just want an array of vectors). How could I go about doing that?

Jaime Over a year ago

You could reshape your array after rolling the axis. If the shape is (rows, cols, 2) simply do thisArray = thisArray.reshape(rows, cols*2), or the equivalent thisArray = thisArray.reshape(rows, -1). Because of your array not being contiguous, this reshaping cannot be done without copying the array. Shouldn't be an issue unless your array is huge.

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