Sort a numpy array by another array, along a particular axis

Question

Similar to this answer, I have a pair of 3D numpy arrays, a and b, and I want to sort the entries of b by the values of a. Unlike this answer, I want to sort only along one axis of the arrays.

My naive reading of the numpy.argsort() documentation:

Returns
-------
index_array : ndarray, int
    Array of indices that sort `a` along the specified axis.
    In other words, ``a[index_array]`` yields a sorted `a`.

led me to believe that I could do my sort with the following code:

import numpy

a = numpy.zeros((3, 3, 3))
a += numpy.array((1, 3, 2)).reshape((3, 1, 1))
print "a"
print a
"""
[[[ 1.  1.  1.]
  [ 1.  1.  1.]
  [ 1.  1.  1.]]

 [[ 3.  3.  3.]
  [ 3.  3.  3.]
  [ 3.  3.  3.]]

 [[ 2.  2.  2.]
  [ 2.  2.  2.]
  [ 2.  2.  2.]]]
"""
b = numpy.arange(3*3*3).reshape((3, 3, 3))
print "b"
print b
"""
[[[ 0  1  2]
  [ 3  4  5]
  [ 6  7  8]]

 [[ 9 10 11]
  [12 13 14]
  [15 16 17]]

 [[18 19 20]
  [21 22 23]
  [24 25 26]]]
"""
print "a, sorted"
print numpy.sort(a, axis=0)
"""
[[[ 1.  1.  1.]
  [ 1.  1.  1.]
  [ 1.  1.  1.]]

 [[ 2.  2.  2.]
  [ 2.  2.  2.]
  [ 2.  2.  2.]]

 [[ 3.  3.  3.]
  [ 3.  3.  3.]
  [ 3.  3.  3.]]]
"""

##This isnt' working how I'd like
sort_indices = numpy.argsort(a, axis=0)
c = b[sort_indices]
"""
Desired output:

[[[ 0  1  2]
  [ 3  4  5]
  [ 6  7  8]]

 [[18 19 20]
  [21 22 23]
  [24 25 26]]

 [[ 9 10 11]
  [12 13 14]
  [15 16 17]]]
"""
print "Desired shape of b[sort_indices]: (3, 3, 3)."
print "Actual shape of b[sort_indices]:"
print c.shape
"""
(3, 3, 3, 3, 3)
"""

What’s the right way to do this?

Asked By: Andrew

||

Source

Answer 1

You still have to supply indices for the other two dimensions for this to work correctly.

>>> a = numpy.zeros((3, 3, 3))
>>> a += numpy.array((1, 3, 2)).reshape((3, 1, 1))
>>> b = numpy.arange(3*3*3).reshape((3, 3, 3))
>>> sort_indices = numpy.argsort(a, axis=0)
>>> static_indices = numpy.indices((3, 3, 3))
>>> b[sort_indices, static_indices[1], static_indices[2]]
array([[[ 0,  1,  2],
        [ 3,  4,  5],
        [ 6,  7,  8]],

       [[18, 19, 20],
        [21, 22, 23],
        [24, 25, 26]],

       [[ 9, 10, 11],
        [12, 13, 14],
        [15, 16, 17]]])

numpy.indices calculates the indices of each axis of the array when “flattened” through the other two axes (or n – 1 axes where n = total number of axes). In other words, this (apologies for the long post):

>>> static_indices
array([[[[0, 0, 0],
         [0, 0, 0],
         [0, 0, 0]],

        [[1, 1, 1],
         [1, 1, 1],
         [1, 1, 1]],

        [[2, 2, 2],
         [2, 2, 2],
         [2, 2, 2]]],


       [[[0, 0, 0],
         [1, 1, 1],
         [2, 2, 2]],

        [[0, 0, 0],
         [1, 1, 1],
         [2, 2, 2]],

        [[0, 0, 0],
         [1, 1, 1],
         [2, 2, 2]]],


       [[[0, 1, 2],
         [0, 1, 2],
         [0, 1, 2]],

        [[0, 1, 2],
         [0, 1, 2],
         [0, 1, 2]],

        [[0, 1, 2],
         [0, 1, 2],
         [0, 1, 2]]]])

These are the identity indices for each axis; when used to index b, they recreate b.

>>> b[static_indices[0], static_indices[1], static_indices[2]]
array([[[ 0,  1,  2],
        [ 3,  4,  5],
        [ 6,  7,  8]],

       [[ 9, 10, 11],
        [12, 13, 14],
        [15, 16, 17]],

       [[18, 19, 20],
        [21, 22, 23],
        [24, 25, 26]]])

As an alternative to numpy.indices, you could use numpy.ogrid, as unutbu suggests. Since the object generated by ogrid is smaller, I’ll create all three axes, just for consistency sake, but note unutbu’s comment for a way to do this by generating only two.

>>> static_indices = numpy.ogrid[0:a.shape[0], 0:a.shape[1], 0:a.shape[2]]
>>> a[sort_indices, static_indices[1], static_indices[2]]
array([[[ 1.,  1.,  1.],
        [ 1.,  1.,  1.],
        [ 1.,  1.,  1.]],

       [[ 2.,  2.,  2.],
        [ 2.,  2.,  2.],
        [ 2.,  2.,  2.]],

       [[ 3.,  3.,  3.],
        [ 3.,  3.,  3.],
        [ 3.,  3.,  3.]]])

Answered By: senderle

Answer 2

numpy.take_along_axis() does it, and presumably without unnecessary memory usage:

import numpy
a = numpy.zeros((3, 3, 3))
a += numpy.array((1, 3, 2)).reshape((3, 1, 1))
b = numpy.arange(3*3*3).reshape((3, 3, 3))
sort_indices = numpy.argsort(a, axis=0)
c = numpy.take_along_axis(b, sort_indices, axis=0)
print(c)
"""
[[[ 0  1  2]
  [ 3  4  5]
  [ 6  7  8]]

 [[18 19 20]
  [21 22 23]
  [24 25 26]]

 [[ 9 10 11]
  [12 13 14]
  [15 16 17]]]
"""

Answered By: Georges

Sort a numpy array by another array, along a particular axis

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