[英]Is there an equivalent to R apply function in Python?
I am trying to find the Python equivalent to R's apply
function but with multidimensional arrays.我试图找到与 R 的
apply
函数等效但具有多维数组的 Python。
For example, when called the following code:例如,当调用以下代码时:
z <- array(1, dim = 2:4)
apply(z, 1, sum)
The result is:结果是:
[1] 12 12
and when called with two values for margin:当使用两个保证金值调用时:
apply(z, c(1,2), sum)
The result is:结果是:
[,1] [,2] [,3]
[1,] 4 4 4
[2,] 4 4 4
I found that the sum
function in numpy can be used, but not in the same consistent way:我发现可以使用 numpy 中的
sum
函数,但不是以相同的一致方式:
For example:例如:
import numpy as np
xx= np.ones((2,3,4))
np.sum(xx,axis=(1,2))
The result is:结果是:
array([12., 12.])
but I can't find a function that equivalent to apply
in its manner specifically when dealing with margin=c(1,2)
.但在处理
margin=c(1,2)
时,我找不到一个等效于以它的方式apply
的函数。 Could anyone help?有人可以帮忙吗?
The equivalent in NumPy is: NumPy中的等效项是:
xx.sum(axis=2)
That is, you are summing over axis 2 (the last dimension), which as its length is 4, leaves the other two dimensions (2,3) as the shape of the result: 也就是说,您要对轴2(最后一个尺寸)求和,其长度为4,剩下的两个尺寸(2,3)作为结果的形状:
array([[4., 4., 4.],
[4., 4., 4.]])
Perhaps a more literal translation of your R code would be: 您的R代码的更直接的翻译可能是:
np.apply_over_axes(np.sum, xx, 2)
Which gives a similar result but transposed. 给出相似的结果,但转置。 This is likely to be slower, however, and is not idiomatic unless the actual operation you're performing is something more complicated than sum.
但是,这可能会比较慢,并且不是惯用语言,除非您要执行的实际操作比总和要复杂得多。
np.apply_over_axes
is different from R's apply
in several ways. np.apply_over_axes
在几个方面与 R 的apply
不同。
First, np.apply_over_axes
needs collapsing axes to be specified, whereas R's apply
needs remaining axes to be specified.首先,
np.apply_over_axes
需要指定折叠轴,而 R 的apply
需要指定剩余的轴。
Secondly, np.apply_over_axes
applies function iteratively as the documentation stated below.其次,
np.apply_over_axes
反复应用功能的文档中另有说明。 The result is the same for np.sum
but it could be different for other functions. np.sum
的结果相同,但其他函数的结果可能不同。
func is called as res = func(a, axis), where axis is the first element of axes.
func 被称为 res = func(a,axis),其中轴是轴的第一个元素。 The result res of the function call must have either the same dimensions as a or one less dimension.
函数调用的结果 res 必须与 a 具有相同的维度或少一个维度。 If res has one less dimension than a, a dimension is inserted before axis.
如果 res 比 a 少一个维度,则在轴之前插入一个维度。 The call to func is then repeated for each axis in axes, with res as the first argument.
然后对轴中的每个轴重复调用 func,将 res 作为第一个参数。
And the func for np.apply_over_axes
needs to be in particular format and the return of func needs to be in particular shape for np.apply_over_axes
to perform correctly.并且
np.apply_over_axes
的 func 需要采用特定格式,并且 func 的返回需要采用特定形状,以便np.apply_over_axes
正确执行。
Here's an example how np.apply_over_axes
fails这是
np.apply_over_axes
如何失败的示例
>>> arr.shape
(5, 4, 3, 2)
>>> np.apply_over_axes(np.mean, arr, (0,1))
array([[[[ 0.05856732, -0.14844212],
[ 0.34214183, 0.24319846],
[-0.04807454, 0.04752829]]]])
>>> np_mean = lambda x: np.mean(x)
>>> np.apply_over_axes(np_mean, arr, (0,1))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<__array_function__ internals>", line 5, in apply_over_axes
File "/Users/kwhkim/opt/miniconda3/envs/rtopython2-pip/lib/python3.8/site-packages/numpy/lib/shape_base.py", line 495, in apply_over_axes
res = func(*args)
TypeError: <lambda>() takes 1 positional argument but 2 were given
Since there seems to be no equivalent function in Python, I made a function that is similar to R's apply
由于Python中好像没有等价的函数,所以我做了一个类似于R的
apply
的函数
def np_apply(arr, axes_remain, fun, *args, **kwargs):
axes_remain = tuple(set(axes_remain))
arr_shape = arr.shape
axes_to_move = set(range(len(arr.shape)))
for axis in axes_remain:
axes_to_move.remove(axis)
axes_to_move = tuple(axes_to_move)
arr, axes_to_move
arr2 = np.moveaxis(arr, axes_to_move, [-x for x in list(range(1,len(axes_to_move)+1))]).copy()
#if arr2.flags.c_contiguous:
arr2 = arr2.reshape([arr_shape[x] for x in axes_remain]+[-1])
return np.apply_along_axis(fun, -1, arr2, *args, **kwargs)
It works fine at least for the sample example as above(not exactly the same as the result above but math.close()
returns True for nearly all elements)它至少对于上面的示例示例工作正常(与上面的结果不完全相同,但
math.close()
对几乎所有元素都返回 True)
>>> np_apply(arr, (2,3), np.mean)
array([[ 0.05856732, -0.14844212],
[ 0.34214183, 0.24319846],
[-0.04807454, 0.04752829]])
>>> np_apply(arr, (2,3), np_mean)
array([[ 0.05856732, -0.14844212],
[ 0.34214183, 0.24319846],
[-0.04807454, 0.04752829]])
For the function to work smoothly for large multidimensional array, it needs to be optimized.为了使函数在大型多维数组中顺利工作,需要对其进行优化。 For instance, array should be prevented from copying.
例如,应该防止数组复制。
Anyway it seems to work as a proof-of-concept and I hope it helps.无论如何,它似乎可以作为概念验证,我希望它有所帮助。
PS) arr
is generated by arr = np.random.normal(0,1,(5,4,3,2))
PS)
arr
由arr = np.random.normal(0,1,(5,4,3,2))
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