Python access all entrys from one dimension in a multidimensional numpy array - python

I would like to manipulate the data of all entries of a complicated 3d numpy array. I want all entries of all subarrays in the X-Y-Position. I know Matlab can do something like that (with the variable indicator : for everything) I indicated that below with DARK[:][1][1]. Which basically mean I want the second entry from the second the column in all sub arrays. Is there a way to do this in python?
import numpy
# Creating a dummy variable of the type I deal with (If this looks crappy sorry, the variable actually comes from the output of d = pyfits.getdata()):
a = []
for i in range(3):
d = numpy.array([[i, 2*i], [3*i, 4*i]])
a.append(d)
print a
# Pseudo code:
print 'Second row, second column: ', a[:][1][1]
I expect a result like this:
[array([[ 0, 0],[ 0, 0]]),
array([[ 1, 2],[ 3, 4]]),
array([[ 2, 4],[ 6, 8]])]
Second row, second column: [0, 4, 8]

You can do this using slightly different syntax.
import numpy as np
a = np.arange(27).reshape(3,3,3) # Create a 3x3x3 3d array
print("3d Array:")
print(a)
print("Second Row, Second Column: ", a[:,1,1])
Output:
>>> 3d 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]]]
>>> Second Row, Second Column: [ 4 13 22]

Found the solution, thanks Divakar and eeScott:
import numpy as np
# Creating a dummy variable of the type I deal with (If this looks crappy sorry, the variable actually comes from the output of d = pyfits.getdata()):
a = []
for i in range(3):
d = np.array([[i, 2*i], [3*i, 4*i]])
a.append(d)
# print variable
print np.array(a)
print 'Second row, second column: ', np.array(a)[:, 1, 1]
# Alternative solution:
a = np.asarray(a)
print a
print 'Second row, second column: ', a[:,1,1]
Result:
[[[0 0][0 0]]
[[1 2][3 4]]
[[2 4][6 8]]]
Second row, second column: [0 4 8]

Related

In python numpy, how to replace some rows in array A with array B if we know the index

In python numpy, how to replace some rows in array A with array B if we know the index.
For example
we have
a = np.array([[1,2],[3,4],[5,6]])
b = np.array([[10,10],[1000, 1000]])
index = [0,2]
I want to change a to
a = np.array([[10,10],[3,4],[1000,1000]])
I have considered the funtion np.where but it need to create the bool condition, not very convenient,
I would do it following way
import numpy as np
a = np.array([[1,2],[3,4],[5,6]])
b = np.array([[10,10],[1000, 1000]])
index = [0,2]
a[index] = b
print(a)
gives output
[[ 10 10]
[ 3 4]
[1000 1000]]
You can use :
a[index] = b
For example :
import numpy as np
a = np.array([[1,2],[3,4],[5,6]])
b = np.array([[10,10],[1000, 1000]])
index = [0,2]
a[index] = b
print(a)
Result :
[[ 10 10]
[ 3 4]
[1000 1000]]
In Python's NumPy library, you can use the numpy.put() method to replace some rows in array A with array B if you know the index. Here's an example:
import numpy as np
# Initialize array A
A = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
# Initialize array B
B = np.array([[10, 20, 30], [40, 50, 60]])
# Indices of the rows to be replaced in array A
indices = [0, 1]
# Replace rows in array A with rows in array B
np.put(A, indices, B)
print(A)
In this example, the first two rows in array A are replaced with the first two rows in array B, so the output will be
[[10 20 30]
[40 50 60]
[ 7 8 9]]
Simply a[indices] = b or if you want to be more fancy np.put(a, indices, b)

Substitute row in Numpy if a condition is met - Variation

I am still figuring out Numpy syntax! I have something that works but there must be a more concise way to perform this task. In the example below, I replace selected rows of an array with new entries, where the condition is just on one element.
import numpy as np
big_array = np.random.randint(10, size=(5, 2)) # multi-dimension array
print(big_array)
bad_values = np.less_equal(big_array[:,0], 4) # condition value in one dimension
bad_rows = np.nonzero(bad_values)[0] # indexes to change, e.g. rows
print(f'these are the rows to replace {bad_rows}')
new_rows = np.random.randint(10, size=((bad_rows.size),2))+10 # smaller multi-dim array
np.put(big_array[:,0],bad_rows,y[:,0]) # should be a single line to combine this
np.put(big_array[:,1],bad_rows,y[:,1]) # with this?
print(big_array)
sample output that I want might look like
[[2 4]
[5 9]
[6 6]
[6 7]
[0 6]]
these are the rows to replace [0 4]
[[16 17]
[ 5 9]
[ 6 6]
[ 6 7]
[18 17]]
I don't know how to format put for arguments with different dimensions. This seems like it should be a one-liner. (If I try where I get length issues broadcasting.) What am I missing?

Can't append numpy arrays after for loop?

After a for loop, I can not append each iteration into a single array:
in:
for a in l:
arr = np.asarray(a_lis)
print(arr)
How can I append and return in a single array the above three arrays?:
[[ 0.55133 0.58122 0.66129032 0.67562724 0.69354839 0.70609319
0.6702509 0.63799283 0.61827957 0.6155914 0.60842294 0.60215054
0.59946237 0.625448 0.60215054 0.60304659 0.59856631 0.59677419
0.59408602 0.61021505]
[ 0.58691756 0.6784946 0.64964158 0.66397849 0.67114695 0.66935484
0.67293907 0.66845878 0.65143369 0.640681 0.63530466 0.6344086
0.6281362 0.6281362 0.62634409 0.6281362 0.62903226 0.63799283
0.63709677 0.6978495]
[ 0.505018 0.53405018 0.59408602 0.65143369 0.66577061 0.66487455
0.65412186 0.64964158 0.64157706 0.63082437 0.62634409 0.6218638
0.62007168 0.6648746 0.62096774 0.62007168 0.62096774 0.62007168
0.62275986 0.81362 ]]
I tried to append as a list, using numpy's append, merge, and hstack. None of them worked. Any idea of how to get the previous output?
Use numpy.concatenate to join the arrays:
import numpy as np
a = np.array([[1, 2, 3, 4]])
b = np.array([[5, 6, 7, 8]])
arr = np.concatenate((a, b), axis=0)
print(arr)
# [[1 2 3 4]
# [5 6 7 8]]
Edit1: To do it inside the array (as mentioned in the comment) you can use numpy.vstack:
import numpy as np
for i in range(0, 3):
a = np.random.randint(0, 10, size=4)
if i == 0:
arr = a
else:
arr = np.vstack((arr, a))
print(arr)
# [[1 1 8 7]
# [2 4 9 1]
# [8 4 7 5]]
Edit2: Citing Iguananaut from the comments:
That said, using concatenate repeatedly can be costly. If you know the
size of the output in advance it's better to pre-allocate an array and
fill it as you go.

NumPy random shuffle rows independently

I have the following array:
import numpy as np
a = np.array([[ 1, 2, 3],
[ 1, 2, 3],
[ 1, 2, 3]])
I understand that np.random.shuffle(a.T) will shuffle the array along the row, but what I need is for it to shuffe each row idependently. How can this be done in numpy? Speed is critical as there will be several million rows.
For this specific problem, each row will contain the same starting population.
import numpy as np
np.random.seed(2018)
def scramble(a, axis=-1):
"""
Return an array with the values of `a` independently shuffled along the
given axis
"""
b = a.swapaxes(axis, -1)
n = a.shape[axis]
idx = np.random.choice(n, n, replace=False)
b = b[..., idx]
return b.swapaxes(axis, -1)
a = a = np.arange(4*9).reshape(4, 9)
# 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],
# [27, 28, 29, 30, 31, 32, 33, 34, 35]])
print(scramble(a, axis=1))
yields
[[ 3 8 7 0 4 5 1 2 6]
[12 17 16 9 13 14 10 11 15]
[21 26 25 18 22 23 19 20 24]
[30 35 34 27 31 32 28 29 33]]
while scrambling along the 0-axis:
print(scramble(a, axis=0))
yields
[[18 19 20 21 22 23 24 25 26]
[ 0 1 2 3 4 5 6 7 8]
[27 28 29 30 31 32 33 34 35]
[ 9 10 11 12 13 14 15 16 17]]
This works by first swapping the target axis with the last axis:
b = a.swapaxes(axis, -1)
This is a common trick used to standardize code which deals with one axis.
It reduces the general case to the specific case of dealing with the last axis.
Since in NumPy version 1.10 or higher swapaxes returns a view, there is no copying involved and so calling swapaxes is very quick.
Now we can generate a new index order for the last axis:
n = a.shape[axis]
idx = np.random.choice(n, n, replace=False)
Now we can shuffle b (independently along the last axis):
b = b[..., idx]
and then reverse the swapaxes to return an a-shaped result:
return b.swapaxes(axis, -1)
If you don't want a return value and want to operate on the array directly, you can specify the indices to shuffle.
>>> import numpy as np
>>>
>>>
>>> a = np.array([[1,2,3], [1,2,3], [1,2,3]])
>>>
>>> # Shuffle row `2` independently
>>> np.random.shuffle(a[2])
>>> a
array([[1, 2, 3],
[1, 2, 3],
[3, 2, 1]])
>>>
>>> # Shuffle column `0` independently
>>> np.random.shuffle(a[:,0])
>>> a
array([[3, 2, 3],
[1, 2, 3],
[1, 2, 1]])
If you want a return value as well, you can use numpy.random.permutation, in which case replace np.random.shuffle(a[n]) with a[n] = np.random.permutation(a[n]).
Warning, do not do a[n] = np.random.shuffle(a[n]). shuffle does not return anything, so the row/column you end up "shuffling" will be filled with nan instead.
Good answer above. But I will throw in a quick and dirty way:
a = np.array([[1,2,3], [1,2,3], [1,2,3]])
ignore_list_outpput = [np.random.shuffle(x) for x in a]
Then, a can be something like this
array([[2, 1, 3],
[4, 6, 5],
[9, 7, 8]])
Not very elegant but you can get this job done with just one short line.
Building on my comment to #Hun's answer, here's the fastest way to do this:
def shuffle_along(X):
"""Minimal in place independent-row shuffler."""
[np.random.shuffle(x) for x in X]
This works in-place and can only shuffle rows. If you need more options:
def shuffle_along(X, axis=0, inline=False):
"""More elaborate version of the above."""
if not inline:
X = X.copy()
if axis == 0:
[np.random.shuffle(x) for x in X]
if axis == 1:
[np.random.shuffle(x) for x in X.T]
if not inline:
return X
This, however, has the limitation of only working on 2d-arrays. For higher dimensional tensors, I would use:
def shuffle_along(X, axis=0, inline=True):
"""Shuffle along any axis of a tensor."""
if not inline:
X = X.copy()
np.apply_along_axis(np.random.shuffle, axis, X) # <-- I just changed this
if not inline:
return X
You can do it with numpy without any loop or extra function, and much more faster. E. g., we have an array of size (2, 6) and we want a sub array (2,2) with independent random index for each column.
import numpy as np
test = np.array([[1, 1],
[2, 2],
[0.5, 0.5],
[0.3, 0.3],
[4, 4],
[7, 7]])
id_rnd = np.random.randint(6, size=(2, 2)) # select random numbers, use choice and range if don want replacement.
new = np.take_along_axis(test, id_rnd, axis=0)
Out:
array([[2. , 2. ],
[0.5, 2. ]])
It works for any number of dimensions.
As of NumPy 1.20.0 released in January 2021 we have a permuted() method on the new Generator type (introduced with the new random API in NumPy 1.17.0, released in July 2019). This does exactly what you need:
import numpy as np
rng = np.random.default_rng()
a = np.array([
[1, 2, 3],
[1, 2, 3],
[1, 2, 3],
])
shuffled = rng.permuted(a, axis=1)
This gives you something like
>>> print(shuffled)
[[2 3 1]
[1 3 2]
[2 1 3]]
As you can see, the rows are permuted independently. This is in sharp contrast with both rng.permutation() and rng.shuffle().
If you want an in-place update you can pass the original array as the out keyword argument. And you can use the axis keyword argument to choose the direction along which to shuffle your array.

Operations on 'N' dimensional numpy arrays

I am attempting to generalize some Python code to operate on arrays of arbitrary dimension. The operations are applied to each vector in the array. So for a 1D array, there is simply one operation, for a 2-D array it would be both row and column-wise (linearly, so order does not matter). For example, a 1D array (a) is simple:
b = operation(a)
where 'operation' is expecting a 1D array. For a 2D array, the operation might proceed as
for ii in range(0,a.shape[0]):
b[ii,:] = operation(a[ii,:])
for jj in range(0,b.shape[1]):
c[:,ii] = operation(b[:,ii])
I would like to make this general where I do not need to know the dimension of the array beforehand, and not have a large set of if/elif statements for each possible dimension.
Solutions that are general for 1 or 2 dimensions are ok, though a completely general solution would be preferred. In reality, I do not imagine needing this for any dimension higher than 2, but if I can see a general example I will learn something!
Extra information:
I have a matlab code that uses cells to do something similar, but I do not fully understand how it works. In this example, each vector is rearranged (basically the same function as fftshift in numpy.fft). Not sure if this helps, but it operates on an array of arbitrary dimension.
function aout=foldfft(ain)
nd = ndims(ain);
for k = 1:nd
nx = size(ain,k);
kx = floor(nx/2);
idx{k} = [kx:nx 1:kx-1];
end
aout = ain(idx{:});
In Octave, your MATLAB code does:
octave:19> size(ain)
ans =
2 3 4
octave:20> idx
idx =
{
[1,1] =
1 2
[1,2] =
1 2 3
[1,3] =
2 3 4 1
}
and then it uses the idx cell array to index ain. With these dimensions it 'rolls' the size 4 dimension.
For 5 and 6 the index lists would be:
2 3 4 5 1
3 4 5 6 1 2
The equivalent in numpy is:
In [161]: ain=np.arange(2*3*4).reshape(2,3,4)
In [162]: idx=np.ix_([0,1],[0,1,2],[1,2,3,0])
In [163]: idx
Out[163]:
(array([[[0]],
[[1]]]), array([[[0],
[1],
[2]]]), array([[[1, 2, 3, 0]]]))
In [164]: ain[idx]
Out[164]:
array([[[ 1, 2, 3, 0],
[ 5, 6, 7, 4],
[ 9, 10, 11, 8]],
[[13, 14, 15, 12],
[17, 18, 19, 16],
[21, 22, 23, 20]]])
Besides the 0 based indexing, I used np.ix_ to reshape the indexes. MATLAB and numpy use different syntax to index blocks of values.
The next step is to construct [0,1],[0,1,2],[1,2,3,0] with code, a straight forward translation.
I can use np.r_ as a short cut for turning 2 slices into an index array:
In [201]: idx=[]
In [202]: for nx in ain.shape:
kx = int(np.floor(nx/2.))
kx = kx-1;
idx.append(np.r_[kx:nx, 0:kx])
.....:
In [203]: idx
Out[203]: [array([0, 1]), array([0, 1, 2]), array([1, 2, 3, 0])]
and pass this through np.ix_ to make the appropriate index tuple:
In [204]: ain[np.ix_(*idx)]
Out[204]:
array([[[ 1, 2, 3, 0],
[ 5, 6, 7, 4],
[ 9, 10, 11, 8]],
[[13, 14, 15, 12],
[17, 18, 19, 16],
[21, 22, 23, 20]]])
In this case, where 2 dimensions don't roll anything, slice(None) could replace those:
In [210]: idx=(slice(None),slice(None),[1,2,3,0])
In [211]: ain[idx]
======================
np.roll does:
indexes = concatenate((arange(n - shift, n), arange(n - shift)))
res = a.take(indexes, axis)
np.apply_along_axis is another function that constructs an index array (and turns it into a tuple for indexing).
If you are looking for a programmatic way to index the k-th dimension an n-dimensional array, then numpy.take might help you.
An implementation of foldfft is given below as an example:
In[1]:
import numpy as np
def foldfft(ain):
result = ain
nd = len(ain.shape)
for k in range(nd):
nx = ain.shape[k]
kx = (nx+1)//2
shifted_index = list(range(kx,nx)) + list(range(kx))
result = np.take(result, shifted_index, k)
return result
a = np.indices([3,3])
print("Shape of a = ", a.shape)
print("\nStarting array:\n\n", a)
print("\nFolded array:\n\n", foldfft(a))
Out[1]:
Shape of a = (2, 3, 3)
Starting array:
[[[0 0 0]
[1 1 1]
[2 2 2]]
[[0 1 2]
[0 1 2]
[0 1 2]]]
Folded array:
[[[2 0 1]
[2 0 1]
[2 0 1]]
[[2 2 2]
[0 0 0]
[1 1 1]]]
You could use numpy.ndarray.flat, which allows you to linearly iterate over a n dimensional numpy array. Your code should then look something like this:
b = np.asarray(x)
for i in range(len(x.flat)):
b.flat[i] = operation(x.flat[i])
The folks above provided multiple appropriate solutions. For completeness, here is my final solution. In this toy example for the case of 3 dimensions, the function 'ops' replaces the first and last element of a vector with 1.
import numpy as np
def ops(s):
s[0]=1
s[-1]=1
return s
a = np.random.rand(4,4,3)
print '------'
print 'Array a'
print a
print '------'
for ii in np.arange(a.ndim):
a = np.apply_along_axis(ops,ii,a)
print '------'
print ' Axis',str(ii)
print a
print '------'
print ' '
The resulting 3D array has a 1 in every element on the 'border' with the numbers in the middle of the array unchanged. This is of course a toy example; however ops could be any arbitrary function that operates on a 1D vector.
Flattening the vector will also work; I chose not to pursue that simply because the book-keeping is more difficult and apply_along_axis is the simplest approach.
apply_along_axis reference page

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