Is there a more pythonic/numpythonic way to do some sort of nested/hierarchical slicing, i.e. a prettier version of this:
_sum = 0
for i in np.arange(n):
_sum += someFunc(A[i,:])
Basically I would like to map someFunc (which takes arrays of any shape and returns a number) over the rows and then sum the results.
I have been thinking about np.sum(someFunc(A[:,:])), but according to my understanding this will just map someFuncover the whole array.
If I understood correctly, you could use a list comprehension like this:
sum([someFunc(A[i:]) for i in np.arange(n)])
Define a function to count 1's in an array:
def foo(x):
return (x==1).sum()
and a 2d array:
In [431]: X=np.array([[1,0,2],[3,1,1],[0,2,3]])
I can apply it iteratively to rows
In [432]: [foo(i) for i in X] # iterate on 1st dimension
Out[432]: [1, 2, 0]
In [433]: [foo(X[i,:]) for i in range(3)]
Out[433]: [1, 2, 0]
and get the total count with sum (here the Python sum)
In [434]: sum([foo(X[i,:]) for i in range(3)])
Out[434]: 3
As written foo gets the same thing with applied to the whole array
In [435]: foo(X)
Out[435]: 3
and for row counts, use the np.sum axis control:
In [440]: np.sum(X==1, axis=1)
Out[440]: array([1, 2, 0])
apply_along_axis can to the same sort of row iteration:
In [438]: np.apply_along_axis(foo,1,X)
Out[438]: array([1, 2, 0])
but for this it is overkill. It's more useful with 3d or larger arrays where it is awkward to iterate over all dimensions except the nth one. It's never faster than doing your own iteration.
It's clearly best if you can write the function to work on the whole array. But if you must iterate on rows, there aren't any magical solutions. vectorize and frompyfunc wrap functions that work with scalar values, not 1d arrays. Some row problems are solved by casting the rows as larger dtype objects (e.g. unique rows).
Related
Let's say I have a 2-d tensor:
x = torch.Tensor([[1, 2], [3, 4]])
Is there an efficient way to apply one function to the first 'row' [1, 2] and apply a second different function to the second row [3, 4]? (Doesn't have to be a row, could be across any dimension)
At the moment, I use the following code: Say I have my two functions, f and g, for example,
def f(z):
return 2 * z
def g(z):
return 0.5 * z
Then, to apply them to seperate rows I would do:
torch.cat([f(x[0]).unsqueeze(0), g(x[1]).unsqueeze(0)], dim = 0)
which gives the desired tensor [[2, 4], [1.5, 2]].
Obviously, in this 2-d example this solution is fine, but it seems a bit clunky. Is there a better way of doing this? Particularly in higher dimensions or when there are a large number of elements in the chosen dimension
A handy tip is to slice instead of selecting to avoid the unsqueeze step. Indeed, notice how x[:1] keeps the indexed dimension compared to x[0].
This way you can perform the desired operation in a slightly shorter form:
>>> torch.vstack((f(x[:1]), g(x[1:])))
Optionally you can use vstack to not have to provide dim=0 to torch.stack.
Alternatively, you can use a helper function that will apply both f and g:
>>> fn = lambda a,b: (f(a), g(b))
And split the tensor inline with torch.Tensor.split:
>>> torch.vstack(fn(*x.split(1)))
My array looks like this:
a = ([1,2],[2,3],[4,5],[3,8])
I did the following to delete odd indexes :
a = [v for i, v in enumerate(a) if i % 2 == 0]
but it dives me now two different arrays instead of one two dimensional:
a= [array([1, 2]), array([4, 5])]
How can I keep the same format as the beginning? thank you!
That is as simple as
a[::2]
which yields the lines with even index.
Use numpy array indexing, not comprehensions:
c = a[list(range(0,len(a),2)),:]
If you define c as the output of a list comprehension, it will return a list of one-dimensional numpy arrays. Instead, using the proper indexing maintains the result a numpy array.
Note than instead of "deleting" the odd indices, what we do is specify what to keep: take all lines with an even index (the list(range(0,len(a),2)) part) and for each line take all elements (the : part)
I was playing with numpy array indexing and find this odd behavior. When I index with np.array or list it works as expected:
In[1]: arr = np.arange(10).reshape(5,2)
arr[ [1, 1] ]
Out[1]: array([[2, 3],
[2, 3]])
But when I put tuple, it gives me a single element:
In[1]: arr = np.arange(10).reshape(5,2)
arr[ (1, 1) ]
Out[1]: 3
Also some kind of this strange tuple vs list behavior occurs with arr.flat:
In[1]: arr = np.arange(10).reshape(5,2)
In[2]: arr.flat[ [3, 4] ]
Out[2]: array([3, 4])
In[3]: arr.flat[ (3, 4) ]
Out[3]: IndexError: unsupported iterator index
I can't understand what is going on under the hood? What difference between tuple and list in this case?
Python 3.5.2
NumPy 1.11.1
What's happening is called fancy indexing, or advanced indexing. There's a difference between indexing with slices, or with a list/array. The trick is that multidimensional indexing actually works with tuples due to the implicit tuple syntax:
import numpy as np
arr = np.arange(10).reshape(5,2)
arr[2,1] == arr[(2,1)] # exact same thing: 2,1 matrix element
However, using a list (or array) inside an index expression will behave differently:
arr[[2,1]]
will index into arr with 1, then with 2, so first it fetches arr[2]==arr[2,:], then arr[1]==arr[1,:], and returns these two rows (row 2 and row 1) as the result.
It gets funkier:
print(arr[1:3,0:2])
print(arr[[1,2],[0,1]])
The first one is regular indexing, and it slices rows 1 to 2 and columns 0 to 1 inclusive; giving you a 2x2 subarray. The second one is fancy indexing, it gives you arr[1,0],arr[2,1] in an array, i.e. it indexes selectively into your array using, essentially, the zip() of the index lists.
Now here's why flat works like that: it returns a flatiter of your array. From help(arr.flat):
class flatiter(builtins.object)
| Flat iterator object to iterate over arrays.
|
| A `flatiter` iterator is returned by ``x.flat`` for any array `x`.
| It allows iterating over the array as if it were a 1-D array,
| either in a for-loop or by calling its `next` method.
So the resulting iterator from arr.flat behaves as a 1d array. When you do
arr.flat[ [3, 4] ]
you're accessing two elements of that virtual 1d array using fancy indexing; it works. But when you're trying to do
arr.flat[ (3,4) ]
you're attempting to access the (3,4) element of a 1d (!) array, but this is erroneous. The reason that this doesn't throw an IndexError is probably only due to the fact that arr.flat itself handles this indexing case.
In [387]: arr=np.arange(10).reshape(5,2)
With this list, you are selecting 2 rows from arr
In [388]: arr[[1,1]]
Out[388]:
array([[2, 3],
[2, 3]])
It's the same as if you explicitly marked the column slice (with : or ...)
In [389]: arr[[1,1],:]
Out[389]:
array([[2, 3],
[2, 3]])
Using an array instead of a list works: arr[np.array([1,1]),:]. (It also eliminates some ambiguities.)
With the tuple, the result is the same as if you wrote the indexing without the tuple wrapper. So it selects an element with row index of 1, column index of 1.
In [390]: arr[(1,1)]
Out[390]: 3
In [391]: arr[1,1]
Out[391]: 3
The arr[1,1] is translated by the interpreter to arr.__getitem__((1,1)). As is common in Python 1,1 is shorthand for (1,1).
In the arr.flat cases you are indexing the array as if it were 1d. np.arange(10)[[2,3]] selects 2 items, while np.arange(10)[(2,3)] is 2d indexing, hence the error.
A couple of recent questions touch on a messier corner case. Sometimes the list is treated as a tuple. The discussion might be enlightening, but don't go there if it's confusing.
Advanced slicing when passed list instead of tuple in numpy
numpy indexing: shouldn't trailing Ellipsis be redundant?
I have some physical simulation code, written in python and using numpy/scipy. Profiling the code shows that 38% of the CPU time is spent in a single doubly nested for loop - this seems excessive, so I've been trying to cut it down.
The goal of the loop is to create an array of indices, showing which elements of a 1D array the elements of a 2D array are equal to.
indices[i,j] = where(1D_array == 2D_array[i,j])
As an example, if 1D_array = [7.2, 2.5, 3.9] and
2D_array = [[7.2, 2.5]
[3.9, 7.2]]
We should have
indices = [[0, 1]
[2, 0]]
I currently have this implemented as
for i in range(ni):
for j in range(nj):
out[i, j] = (1D_array - 2D_array[i, j]).argmin()
The argmin is needed as I'm dealing with floating point numbers, and so the equality is not necessarily exact. I know that every number in the 1D array is unique, and that every element in the 2D array has a match, so this approach gives the correct result.
Is there any way of eliminating the double for loop?
Note:
I need the index array to perform the following operation:
f = complex_function(1D_array)
output = f[indices]
This is faster than the alternative, as the 2D array has a size of NxN compared with 1xN for the 1D array, and the 2D array has many repeated values. If anyone can suggest a different way of arriving at the same output without going through an index array, that could also be a solution
In pure Python you can do this using a dictionary in O(N) time, the only time penalty is going to be the Python loop involved:
>>> arr1 = np.array([7.2, 2.5, 3.9])
>>> arr2 = np.array([[7.2, 2.5], [3.9, 7.2]])
>>> indices = dict(np.hstack((arr1[:, None], np.arange(3)[:, None])))
>>> np.fromiter((indices[item] for item in arr2.ravel()), dtype=arr2.dtype).reshape(arr2.shape)
array([[ 0., 1.],
[ 2., 0.]])
The dictionary method that some others have suggest might work, but it requires that you know ahead of time that every element in your target array (the 2d array) has an exact match in your search array (your 1d array). Even when this should be true in principle, you still have to deal with floating point precision issues, for example try this .1 * 3 == .3.
Another approach is to use numpy's searchsorted function. searchsorted takes a sorted 1d search array and any traget array then finds the closest elements in the search array for every item in the target array. I've adapted this answer for your situation, take a look at it for a description of how the find_closest function works.
import numpy as np
def find_closest(A, target):
order = A.argsort()
A = A[order]
idx = A.searchsorted(target)
idx = np.clip(idx, 1, len(A)-1)
left = A[idx-1]
right = A[idx]
idx -= target - left < right - target
return order[idx]
array1d = np.array([7.2, 2.5, 3.9])
array2d = np.array([[7.2, 2.5],
[3.9, 7.2]])
indices = find_closest(array1d, array2d)
print(indices)
# [[0 1]
# [2 0]]
To get rid of the two Python for loops, you can do all of the equality comparisons "in one go" by adding new axes to the arrays (making them broadcastable with each other).
Bear in mind that this produces a new array containing len(arr1)*len(arr2) values. If this is a very big number, this approach could be infeasible depending on the limitations of your memory. Otherwise, it should be reasonably quick:
>>> (arr1[:,np.newaxis] == arr2[:,np.newaxis]).argmax(axis=1)
array([[0, 1],
[2, 0]], dtype=int32)
If you need to get the index of the closest matching value in arr1 instead, use:
np.abs(arr1[:,np.newaxis] - arr2[:,np.newaxis]).argmin(axis=1)
Say that I have 4 numpy arrays
[1,2,3]
[2,3,1]
[3,2,1]
[1,3,2]
In this case, I've determined [1,2,3] is the "minimum array" for my purposes, as it is one of two arrays with lowest value at index 0, and of those two arrays it has the the lowest index 1. If there were more arrays with similar values, I would need to compare the next index values, and so on.
How can I extract the array [1,2,3] in that same order from the pile?
How can I extend that to x arrays of size n?
Thanks
Using the python non-numpy .sort() or sorted() on a list of lists (not numpy arrays) automatically does this e.g.
a = [[1,2,3],[2,3,1],[3,2,1],[1,3,2]]
a.sort()
gives
[[1,2,3],[1,3,2],[2,3,1],[3,2,1]]
The numpy sort seems to only sort the subarrays recursively so it seems the best way would be to convert it to a python list first. Assuming you have an array of arrays you want to pick the minimum of you could get the minimum as
sorted(a.tolist())[0]
As someone pointed out you could also do min(a.tolist()) which uses the same type of comparisons as sort, and would be faster for large arrays (linear vs n log n asymptotic run time).
Here's an idea using numpy:
import numpy
a = numpy.array([[1,2,3],[2,3,1],[3,2,1],[1,3,2]])
col = 0
while a.shape[0] > 1:
b = numpy.argmin(a[:,col:], axis=1)
a = a[b == numpy.min(b)]
col += 1
print a
This checks column by column until only one row is left.
numpy's lexsort is close to what you want. It sorts on the last key first, but that's easy to get around:
>>> a = np.array([[1,2,3],[2,3,1],[3,2,1],[1,3,2]])
>>> order = np.lexsort(a[:, ::-1].T)
>>> order
array([0, 3, 1, 2])
>>> a[order]
array([[1, 2, 3],
[1, 3, 2],
[2, 3, 1],
[3, 2, 1]])