Selecting specific groups of rows from numpy array [duplicate] - python

Given:
test = numpy.array([[1, 2], [3, 4], [5, 6]])
test[i] gives the ith row (e.g. [1, 2]). How do I access the ith column? (e.g. [1, 3, 5]). Also, would this be an expensive operation?


To access column 0:
>>> test[:, 0]
array([1, 3, 5])
To access row 0:
>>> test[0, :]
array([1, 2])
This is covered in Section 1.4 (Indexing) of the NumPy reference. This is quick, at least in my experience. It's certainly much quicker than accessing each element in a loop.


>>> test[:,0]
array([1, 3, 5])
this command gives you a row vector, if you just want to loop over it, it's fine, but if you want to hstack with some other array with dimension 3xN, you will have
ValueError: all the input arrays must have same number of dimensions
while
>>> test[:,[0]]
array([[1],
[3],
[5]])
gives you a column vector, so that you can do concatenate or hstack operation.
e.g.
>>> np.hstack((test, test[:,[0]]))
array([[1, 2, 1],
[3, 4, 3],
[5, 6, 5]])


And if you want to access more than one column at a time you could do:
>>> test = np.arange(9).reshape((3,3))
>>> test
array([[0, 1, 2],
[3, 4, 5],
[6, 7, 8]])
>>> test[:,[0,2]]
array([[0, 2],
[3, 5],
[6, 8]])


You could also transpose and return a row:
In [4]: test.T[0]
Out[4]: array([1, 3, 5])


Although the question has been answered, let me mention some nuances.
Let's say you are interested in the first column of the array
arr = numpy.array([[1, 2],
[3, 4],
[5, 6]])
As you already know from other answers, to get it in the form of "row vector" (array of shape (3,)), you use slicing:
arr_col1_view = arr[:, 1] # creates a view of the 1st column of the arr
arr_col1_copy = arr[:, 1].copy() # creates a copy of the 1st column of the arr
To check if an array is a view or a copy of another array you can do the following:
arr_col1_view.base is arr # True
arr_col1_copy.base is arr # False
see ndarray.base.
Besides the obvious difference between the two (modifying arr_col1_view will affect the arr), the number of byte-steps for traversing each of them is different:
arr_col1_view.strides[0] # 8 bytes
arr_col1_copy.strides[0] # 4 bytes
see strides and this answer.
Why is this important? Imagine that you have a very big array A instead of the arr:
A = np.random.randint(2, size=(10000, 10000), dtype='int32')
A_col1_view = A[:, 1]
A_col1_copy = A[:, 1].copy()
and you want to compute the sum of all the elements of the first column, i.e. A_col1_view.sum() or A_col1_copy.sum(). Using the copied version is much faster:
%timeit A_col1_view.sum() # ~248 µs
%timeit A_col1_copy.sum() # ~12.8 µs
This is due to the different number of strides mentioned before:
A_col1_view.strides[0] # 40000 bytes
A_col1_copy.strides[0] # 4 bytes
Although it might seem that using column copies is better, it is not always true for the reason that making a copy takes time too and uses more memory (in this case it took me approx. 200 µs to create the A_col1_copy). However if we needed the copy in the first place, or we need to do many different operations on a specific column of the array and we are ok with sacrificing memory for speed, then making a copy is the way to go.
In the case we are interested in working mostly with columns, it could be a good idea to create our array in column-major ('F') order instead of the row-major ('C') order (which is the default), and then do the slicing as before to get a column without copying it:
A = np.asfortranarray(A) # or np.array(A, order='F')
A_col1_view = A[:, 1]
A_col1_view.strides[0] # 4 bytes
%timeit A_col1_view.sum() # ~12.6 µs vs ~248 µs
Now, performing the sum operation (or any other) on a column-view is as fast as performing it on a column copy.
Finally let me note that transposing an array and using row-slicing is the same as using the column-slicing on the original array, because transposing is done by just swapping the shape and the strides of the original array.
A[:, 1].strides[0] # 40000 bytes
A.T[1, :].strides[0] # 40000 bytes


To get several and indepent columns, just:
> test[:,[0,2]]
you will get colums 0 and 2


>>> test
array([[0, 1, 2, 3, 4],
[5, 6, 7, 8, 9]])
>>> ncol = test.shape[1]
>>> ncol
5L
Then you can select the 2nd - 4th column this way:
>>> test[0:, 1:(ncol - 1)]
array([[1, 2, 3],
[6, 7, 8]])


This is not multidimensional. It is 2 dimensional array. where you want to access the columns you wish.
test = numpy.array([[1, 2], [3, 4], [5, 6]])
test[:, a:b] # you can provide index in place of a and b

Related

Numpy array indexing with a List: difference between arr[:][li] and arr[:,li]

What is the explanation of the following behavior:
import numpy as np
arr = np.zeros((3, 3))
li = [1,2]
print('output1:', arr[:, li].shape)
print('output2:', arr[:][li].shape)
>>output1: (3, 2)
>>output2: (2, 3)
I would expect output2 to be equal to output1.

Let's use a different array where it's easier to see the difference:
>>> arr = np.arange(9).reshape(3, 3)
>>> arr
array([[0, 1, 2],
[3, 4, 5],
[6, 7, 8]])
The first case arr[:, li] will select all elements from the first dimension (in this case all the rows), then index the array with [1, 2], which means just leaving out the first column:
array([[1, 2],
[4, 5],
[7, 8]])
Hence, the shape of this is (3, 2).
The other case arr[:] will copy the original array, so it doesn't change the shape, therefore it's equvivalent to arr[li], hence the output shape is (2, 3). In general you should avoid double indexing an array, because that might create views twice, which is inefficient.

You are getting the the correct output.
In first line
print('output1:', arr[:, li].shape)
You are printing 2nd and 3rd element of each subarray within arr, thus getting 3 elements each containing 2 values.
In second line
print('output2:', arr[:][li].shape)
You are selecting first the whole array, then from the whole array you select 2nd and 3rd element (each containing 3 elements themselves), thus getting 2 elements each containing 3 values.

The difference can be seen if you examine this code -
import numpy as np
arr = np.arange(9).reshape(3, 3)
li = [1,2]
print('output1:', arr[:, li])
print('output2:', arr[:][li])
This gives -
[[1 2]
[4 5]
[7 8]]
and
[[3 4 5]
[6 7 8]]
When you do arr[:, [1, 2]], what you are saying that you want to take all the rows of the array (: specifies this) and, from that, take column [1, 2].
On the other hand, when you do arr[:], you are referring to the full array first. Out of which you are again taking the first two rows.
Essentially, in the second case, [1 2] is referring to the row axis of the original array while in the first case, it's referring to the column.

Repeat specific row or column of Python numpy 2D array [duplicate]

I'd like to copy a numpy 2D array into a third dimension. For example, given the 2D numpy array:
import numpy as np
arr = np.array([[1, 2], [1, 2]])
# arr.shape = (2, 2)
convert it into a 3D matrix with N such copies in a new dimension. Acting on arr with N=3, the output should be:
new_arr = np.array([[[1, 2], [1,2]],
[[1, 2], [1, 2]],
[[1, 2], [1, 2]]])
# new_arr.shape = (3, 2, 2)

Probably the cleanest way is to use np.repeat:
a = np.array([[1, 2], [1, 2]])
print(a.shape)
# (2, 2)
# indexing with np.newaxis inserts a new 3rd dimension, which we then repeat the
# array along, (you can achieve the same effect by indexing with None, see below)
b = np.repeat(a[:, :, np.newaxis], 3, axis=2)
print(b.shape)
# (2, 2, 3)
print(b[:, :, 0])
# [[1 2]
# [1 2]]
print(b[:, :, 1])
# [[1 2]
# [1 2]]
print(b[:, :, 2])
# [[1 2]
# [1 2]]
Having said that, you can often avoid repeating your arrays altogether by using broadcasting. For example, let's say I wanted to add a (3,) vector:
c = np.array([1, 2, 3])
to a. I could copy the contents of a 3 times in the third dimension, then copy the contents of c twice in both the first and second dimensions, so that both of my arrays were (2, 2, 3), then compute their sum. However, it's much simpler and quicker to do this:
d = a[..., None] + c[None, None, :]
Here, a[..., None] has shape (2, 2, 1) and c[None, None, :] has shape (1, 1, 3)*. When I compute the sum, the result gets 'broadcast' out along the dimensions of size 1, giving me a result of shape (2, 2, 3):
print(d.shape)
# (2, 2, 3)
print(d[..., 0]) # a + c[0]
# [[2 3]
# [2 3]]
print(d[..., 1]) # a + c[1]
# [[3 4]
# [3 4]]
print(d[..., 2]) # a + c[2]
# [[4 5]
# [4 5]]
Broadcasting is a very powerful technique because it avoids the additional overhead involved in creating repeated copies of your input arrays in memory.
* Although I included them for clarity, the None indices into c aren't actually necessary - you could also do a[..., None] + c, i.e. broadcast a (2, 2, 1) array against a (3,) array. This is because if one of the arrays has fewer dimensions than the other then only the trailing dimensions of the two arrays need to be compatible. To give a more complicated example:
a = np.ones((6, 1, 4, 3, 1)) # 6 x 1 x 4 x 3 x 1
b = np.ones((5, 1, 3, 2)) # 5 x 1 x 3 x 2
result = a + b # 6 x 5 x 4 x 3 x 2

Another way is to use numpy.dstack. Supposing that you want to repeat the matrix a num_repeats times:
import numpy as np
b = np.dstack([a]*num_repeats)
The trick is to wrap the matrix a into a list of a single element, then using the * operator to duplicate the elements in this list num_repeats times.
For example, if:
a = np.array([[1, 2], [1, 2]])
num_repeats = 5
This repeats the array of [1 2; 1 2] 5 times in the third dimension. To verify (in IPython):
In [110]: import numpy as np
In [111]: num_repeats = 5
In [112]: a = np.array([[1, 2], [1, 2]])
In [113]: b = np.dstack([a]*num_repeats)
In [114]: b[:,:,0]
Out[114]:
array([[1, 2],
[1, 2]])
In [115]: b[:,:,1]
Out[115]:
array([[1, 2],
[1, 2]])
In [116]: b[:,:,2]
Out[116]:
array([[1, 2],
[1, 2]])
In [117]: b[:,:,3]
Out[117]:
array([[1, 2],
[1, 2]])
In [118]: b[:,:,4]
Out[118]:
array([[1, 2],
[1, 2]])
In [119]: b.shape
Out[119]: (2, 2, 5)
At the end we can see that the shape of the matrix is 2 x 2, with 5 slices in the third dimension.

Use a view and get free runtime! Extend generic n-dim arrays to n+1-dim
Introduced in NumPy 1.10.0, we can leverage numpy.broadcast_to to simply generate a 3D view into the 2D input array. The benefit would be no extra memory overhead and virtually free runtime. This would be essential in cases where the arrays are big and we are okay to work with views. Also, this would work with generic n-dim cases.
I would use the word stack in place of copy, as readers might confuse it with the copying of arrays that creates memory copies.
Stack along first axis
If we want to stack input arr along the first axis, the solution with np.broadcast_to to create 3D view would be -
np.broadcast_to(arr,(3,)+arr.shape) # N = 3 here
Stack along third/last axis
To stack input arr along the third axis, the solution to create 3D view would be -
np.broadcast_to(arr[...,None],arr.shape+(3,))
If we actually need a memory copy, we can always append .copy() there. Hence, the solutions would be -
np.broadcast_to(arr,(3,)+arr.shape).copy()
np.broadcast_to(arr[...,None],arr.shape+(3,)).copy()
Here's how the stacking works for the two cases, shown with their shape information for a sample case -
# Create a sample input array of shape (4,5)
In [55]: arr = np.random.rand(4,5)
# Stack along first axis
In [56]: np.broadcast_to(arr,(3,)+arr.shape).shape
Out[56]: (3, 4, 5)
# Stack along third axis
In [57]: np.broadcast_to(arr[...,None],arr.shape+(3,)).shape
Out[57]: (4, 5, 3)
Same solution(s) would work to extend a n-dim input to n+1-dim view output along the first and last axes. Let's explore some higher dim cases -
3D input case :
In [58]: arr = np.random.rand(4,5,6)
# Stack along first axis
In [59]: np.broadcast_to(arr,(3,)+arr.shape).shape
Out[59]: (3, 4, 5, 6)
# Stack along last axis
In [60]: np.broadcast_to(arr[...,None],arr.shape+(3,)).shape
Out[60]: (4, 5, 6, 3)
4D input case :
In [61]: arr = np.random.rand(4,5,6,7)
# Stack along first axis
In [62]: np.broadcast_to(arr,(3,)+arr.shape).shape
Out[62]: (3, 4, 5, 6, 7)
# Stack along last axis
In [63]: np.broadcast_to(arr[...,None],arr.shape+(3,)).shape
Out[63]: (4, 5, 6, 7, 3)
and so on.
Timings
Let's use a large sample 2D case and get the timings and verify output being a view.
# Sample input array
In [19]: arr = np.random.rand(1000,1000)
Let's prove that the proposed solution is a view indeed. We will use stacking along first axis (results would be very similar for stacking along the third axis) -
In [22]: np.shares_memory(arr, np.broadcast_to(arr,(3,)+arr.shape))
Out[22]: True
Let's get the timings to show that it's virtually free -
In [20]: %timeit np.broadcast_to(arr,(3,)+arr.shape)
100000 loops, best of 3: 3.56 µs per loop
In [21]: %timeit np.broadcast_to(arr,(3000,)+arr.shape)
100000 loops, best of 3: 3.51 µs per loop
Being a view, increasing N from 3 to 3000 changed nothing on timings and both are negligible on timing units. Hence, efficient both on memory and performance!

This can now also be achived using np.tile as follows:
import numpy as np
a = np.array([[1,2],[1,2]])
b = np.tile(a,(3, 1,1))
b.shape
(3,2,2)
b
array([[[1, 2],
[1, 2]],
[[1, 2],
[1, 2]],
[[1, 2],
[1, 2]]])

A=np.array([[1,2],[3,4]])
B=np.asarray([A]*N)
Edit #Mr.F, to preserve dimension order:
B=B.T

Here's a broadcasting example that does exactly what was requested.
a = np.array([[1, 2], [1, 2]])
a=a[:,:,None]
b=np.array([1]*5)[None,None,:]
Then b*a is the desired result and (b*a)[:,:,0] produces array([[1, 2],[1, 2]]), which is the original a, as does (b*a)[:,:,1], etc.

Summarizing the solutions above:
a = np.arange(9).reshape(3,-1)
b = np.repeat(a[:, :, np.newaxis], 5, axis=2)
c = np.dstack([a]*5)
d = np.tile(a, [5,1,1])
e = np.array([a]*5)
f = np.repeat(a[np.newaxis, :, :], 5, axis=0) # np.repeat again
print('b='+ str(b.shape), b[:,:,-1].tolist())
print('c='+ str(c.shape),c[:,:,-1].tolist())
print('d='+ str(d.shape),d[-1,:,:].tolist())
print('e='+ str(e.shape),e[-1,:,:].tolist())
print('f='+ str(f.shape),f[-1,:,:].tolist())
b=(3, 3, 5) [[0, 1, 2], [3, 4, 5], [6, 7, 8]]
c=(3, 3, 5) [[0, 1, 2], [3, 4, 5], [6, 7, 8]]
d=(5, 3, 3) [[0, 1, 2], [3, 4, 5], [6, 7, 8]]
e=(5, 3, 3) [[0, 1, 2], [3, 4, 5], [6, 7, 8]]
f=(5, 3, 3) [[0, 1, 2], [3, 4, 5], [6, 7, 8]]
Good luck

Numpy sort two arrays together with one array as the keys in axis 1 [duplicate]

I'm trying to get the indices to sort a multidimensional array by the last axis, e.g.
>>> a = np.array([[3,1,2],[8,9,2]])
And I'd like indices i such that,
>>> a[i]
array([[1, 2, 3],
[2, 8, 9]])
Based on the documentation of numpy.argsort I thought it should do this, but I'm getting the error:
>>> a[np.argsort(a)]
IndexError: index 2 is out of bounds for axis 0 with size 2
Edit: I need to rearrange other arrays of the same shape (e.g. an array b such that a.shape == b.shape) in the same way... so that
>>> b = np.array([[0,5,4],[3,9,1]])
>>> b[i]
array([[5,4,0],
[9,3,1]])

Solution:
>>> a[np.arange(np.shape(a)[0])[:,np.newaxis], np.argsort(a)]
array([[1, 2, 3],
[2, 8, 9]])
You got it right, though I wouldn't describe it as cheating the indexing.
Maybe this will help make it clearer:
In [544]: i=np.argsort(a,axis=1)
In [545]: i
Out[545]:
array([[1, 2, 0],
[2, 0, 1]])
i is the order that we want, for each row. That is:
In [546]: a[0, i[0,:]]
Out[546]: array([1, 2, 3])
In [547]: a[1, i[1,:]]
Out[547]: array([2, 8, 9])
To do both indexing steps at once, we have to use a 'column' index for the 1st dimension.
In [548]: a[[[0],[1]],i]
Out[548]:
array([[1, 2, 3],
[2, 8, 9]])
Another array that could be paired with i is:
In [560]: j=np.array([[0,0,0],[1,1,1]])
In [561]: j
Out[561]:
array([[0, 0, 0],
[1, 1, 1]])
In [562]: a[j,i]
Out[562]:
array([[1, 2, 3],
[2, 8, 9]])
If i identifies the column for each element, then j specifies the row for each element. The [[0],[1]] column array works just as well because it can be broadcasted against i.
I think of
np.array([[0],
[1]])
as 'short hand' for j. Together they define the source row and column of each element of the new array. They work together, not sequentially.
The full mapping from a to the new array is:
[a[0,1] a[0,2] a[0,0]
a[1,2] a[1,0] a[1,1]]
def foo(a):
i = np.argsort(a, axis=1)
return (np.arange(a.shape[0])[:,None], i)
In [61]: foo(a)
Out[61]:
(array([[0],
[1]]), array([[1, 2, 0],
[2, 0, 1]], dtype=int32))
In [62]: a[foo(a)]
Out[62]:
array([[1, 2, 3],
[2, 8, 9]])

The above answers are now a bit outdated, since new functionality was added in numpy 1.15 to make it simpler; take_along_axis (https://docs.scipy.org/doc/numpy-1.15.1/reference/generated/numpy.take_along_axis.html) allows you to do:
>>> a = np.array([[3,1,2],[8,9,2]])
>>> np.take_along_axis(a, a.argsort(axis=-1), axis=-1)
array([[1 2 3]
[2 8 9]])

I found the answer here, with someone having the same problem. They key is just cheating the indexing to work properly...
>>> a[np.arange(np.shape(a)[0])[:,np.newaxis], np.argsort(a)]
array([[1, 2, 3],
[2, 8, 9]])

You can also use linear indexing, which might be better with performance, like so -
M,N = a.shape
out = b.ravel()[a.argsort(1)+(np.arange(M)[:,None]*N)]
So, a.argsort(1)+(np.arange(M)[:,None]*N) basically are the linear indices that are used to map b to get the desired sorted output for b. The same linear indices could also be used on a for getting the sorted output for a.
Sample run -
In [23]: a = np.array([[3,1,2],[8,9,2]])
In [24]: b = np.array([[0,5,4],[3,9,1]])
In [25]: M,N = a.shape
In [26]: b.ravel()[a.argsort(1)+(np.arange(M)[:,None]*N)]
Out[26]:
array([[5, 4, 0],
[1, 3, 9]])
Rumtime tests -
In [27]: a = np.random.rand(1000,1000)
In [28]: b = np.random.rand(1000,1000)
In [29]: M,N = a.shape
In [30]: %timeit b[np.arange(np.shape(a)[0])[:,np.newaxis], np.argsort(a)]
10 loops, best of 3: 133 ms per loop
In [31]: %timeit b.ravel()[a.argsort(1)+(np.arange(M)[:,None]*N)]
10 loops, best of 3: 96.7 ms per loop

How can I return a column-major iterator for a numpy array?

ndarray objects in numpy have a flat property (e.g. array.flat) that allows one to iterate through its elements. For example:
>>> x = np.arange(1, 7).reshape(2, 3)
>>> x
array([[1, 2, 3],
[4, 5, 6]])
>>> x.flat[3]
4
But how can I return a column-major 1D iterator, so that the example above returns 5 instead of 4?

Approach #1
You can use .ravel('F') to have column major order and then index -
x.ravel('F')[3]
Sample run -
In [100]: x
Out[100]:
array([[1, 2, 3],
[4, 5, 6]])
In [101]: x.ravel('F')[3]
Out[101]: 5
This will create a copy of the entire array before selecting elements -
In [161]: np.may_share_memory(x, x.ravel())
Out[161]: True
In [162]: np.may_share_memory(x, x.ravel('F'))
Out[162]: False
As such this may not the most memory efficient one. For a better one, let's move onto another approach.
Approach #2
We can get the row and column indices from the column-major ordered index and then simply index into the array with it -
x[np.unravel_index(3, np.array(x.shape)[::-1])]
Sample run -
In [147]: x
Out[147]:
array([[1, 2, 3],
[4, 5, 6]])
In [148]: idx = np.unravel_index(3, np.array(x.shape)[::-1])
In [149]: idx
Out[149]: (1, 1) # row, col indices obtained in C order
In [150]: x[idx]
Out[150]: 5
There isn't any copying or flattening or ravel-ing here and uses just an indexing and as such should be efficient both in terms of memory and performance.

Not sure if this is the best way, but it seems that simply
array.T.flat
will give the result I'm looking for. Although I wish there was some appropriate method that I could specify with order='F', which would be easier to understand at a glance.

Numpy remove column in array if first value in column is larger than last

What's an efficient way to remove columns from an NumPy array if the first value is greater than the last value in that column. Let's say I had b:
>>> import numpy as np
>>> b = np.arange(9).reshape(3,3)
>>> b[0,0] = 9
>>> b
array([[9, 1, 2],
[3, 4, 5],
[6, 7, 8]])
And since the b[0,0] > b[-1,0], you would wish to remove the first column and effectively be left with:
array([[1, 2],
[4, 5],
[7, 8]])
What's an efficient way to do this? I've seen it done with rows, with notation like:
b[np.logical_not(np.logical_and(b[:,0] > 20, b[:,0] < 25))]
But not with columns. Also, if transposing could be avoided that would definitely be preferable as I would like to use this on a large data set.

Simply use logical indexing:
new_b = b[:, b[0,:]<=b[-1,:]]

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