Python中是否有SciPy函数或NumPy函数或模块来计算给定特定窗口的1D数组的运行平均值?


有关现成的解决方案,请参见https://scipy-cookbook.readthedocs.io/items/SignalSmooth.html。 它提供了平窗类型的运行平均值。请注意,这比简单的do-it-yourself卷积方法要复杂一些,因为它试图通过反射数据来处理数据开头和结尾的问题(在您的情况下可能有效,也可能无效……)。

首先,你可以试着:

a = np.random.random(100)
plt.plot(a)
b = smooth(a, window='flat')
plt.plot(b)

你可以用以下方法计算运行平均值:

import numpy as np

def runningMean(x, N):
    y = np.zeros((len(x),))
    for ctr in range(len(x)):
         y[ctr] = np.sum(x[ctr:(ctr+N)])
    return y/N

但是速度很慢。

幸运的是,numpy包含一个卷积函数,我们可以用它来加快速度。运行均值相当于将x与一个长度为N的向量进行卷积,其中所有元素都等于1/N。卷积的numpy实现包括起始瞬态,所以你必须删除前N-1点:

def runningMeanFast(x, N):
    return np.convolve(x, np.ones((N,))/N)[(N-1):]

在我的机器上,快速版本要快20-30倍,这取决于输入向量的长度和平均窗口的大小。

请注意,卷积确实包括一个“相同”模式,它似乎应该解决开始的瞬态问题,但它在开始和结束之间分割。


更新:已经提出了更有效的解决方案,scipy的uniform_filter1d可能是“标准”第三方库中最好的,还有一些更新的或专门的库可用。


你可以用np。卷积得到:

np.convolve(x, np.ones(N)/N, mode='valid')

解释

The running mean is a case of the mathematical operation of convolution. For the running mean, you slide a window along the input and compute the mean of the window's contents. For discrete 1D signals, convolution is the same thing, except instead of the mean you compute an arbitrary linear combination, i.e., multiply each element by a corresponding coefficient and add up the results. Those coefficients, one for each position in the window, are sometimes called the convolution kernel. The arithmetic mean of N values is (x_1 + x_2 + ... + x_N) / N, so the corresponding kernel is (1/N, 1/N, ..., 1/N), and that's exactly what we get by using np.ones(N)/N.

边缘

np的模态参数。Convolve指定如何处理边缘。我在这里选择有效模式,因为我认为这是大多数人期望的运行方式,但您可能有其他优先级。下面是一个图表,说明了模式之间的差异:

import numpy as np
import matplotlib.pyplot as plt
modes = ['full', 'same', 'valid']
for m in modes:
    plt.plot(np.convolve(np.ones(200), np.ones(50)/50, mode=m));
plt.axis([-10, 251, -.1, 1.1]);
plt.legend(modes, loc='lower center');
plt.show()


如果你选择自己生成,而不是使用现有的库,请注意浮点错误并尽量减少其影响:

class SumAccumulator:
    def __init__(self):
        self.values = [0]
        self.count = 0

    def add( self, val ):
        self.values.append( val )
        self.count = self.count + 1
        i = self.count
        while i & 0x01:
            i = i >> 1
            v0 = self.values.pop()
            v1 = self.values.pop()
            self.values.append( v0 + v1 )

    def get_total(self):
        return sum( reversed(self.values) )

    def get_size( self ):
        return self.count

如果所有的值都是大致相同的数量级,那么这将通过始终添加大致相似的数量级值来帮助保持精度。


高效的解决方案

卷积比直接的方法好得多,但(我猜)它使用FFT,因此相当慢。但是,下面的方法特别适用于计算运行平均值

def running_mean(x, N):
    cumsum = numpy.cumsum(numpy.insert(x, 0, 0)) 
    return (cumsum[N:] - cumsum[:-N]) / float(N)

要检查的代码

In[3]: x = numpy.random.random(100000)
In[4]: N = 1000
In[5]: %timeit result1 = numpy.convolve(x, numpy.ones((N,))/N, mode='valid')
10 loops, best of 3: 41.4 ms per loop
In[6]: %timeit result2 = running_mean(x, N)
1000 loops, best of 3: 1.04 ms per loop

注意numpy。allclose(result1, result2)为True,两个方法等价。 N越大,时间差异越大。

警告:虽然cumsum更快,但会增加浮点错误,这可能导致您的结果无效/不正确/不可接受

这里的评论指出了这个浮点错误问题,但我在回答中让它更明显。

# demonstrate loss of precision with only 100,000 points
np.random.seed(42)
x = np.random.randn(100000)+1e6
y1 = running_mean_convolve(x, 10)
y2 = running_mean_cumsum(x, 10)
assert np.allclose(y1, y2, rtol=1e-12, atol=0)

the more points you accumulate over the greater the floating point error (so 1e5 points is noticable, 1e6 points is more significant, more than 1e6 and you may want to resetting the accumulators) you can cheat by using np.longdouble but your floating point error still will get significant for relatively large number of points (around >1e5 but depends on your data) you can plot the error and see it increasing relatively fast the convolve solution is slower but does not have this floating point loss of precision the uniform_filter1d solution is faster than this cumsum solution AND does not have this floating point loss of precision


我还没有检查这有多快,但你可以试试:

from collections import deque

cache = deque() # keep track of seen values
n = 10          # window size
A = xrange(100) # some dummy iterable
cum_sum = 0     # initialize cumulative sum

for t, val in enumerate(A, 1):
    cache.append(val)
    cum_sum += val
    if t < n:
        avg = cum_sum / float(t)
    else:                           # if window is saturated,
        cum_sum -= cache.popleft()  # subtract oldest value
        avg = cum_sum / float(n)

更新:下面的例子展示了老熊猫。Rolling_mean函数,该函数在最近版本的pandas中已被删除。该函数调用的现代等价函数将使用pandas.Series.rolling:

In [8]: pd.Series(x).rolling(window=N).mean().iloc[N-1:].values
Out[8]: 
array([ 0.49815397,  0.49844183,  0.49840518, ...,  0.49488191,
        0.49456679,  0.49427121])

pandas比NumPy或SciPy更适合这一点。它的函数rolling_mean很方便地完成了这项工作。当输入是一个数组时,它还返回一个NumPy数组。

使用任何定制的纯Python实现都很难在性能上击败rolling_mean。下面是针对两个提议的解决方案的性能示例:

In [1]: import numpy as np

In [2]: import pandas as pd

In [3]: def running_mean(x, N):
   ...:     cumsum = np.cumsum(np.insert(x, 0, 0)) 
   ...:     return (cumsum[N:] - cumsum[:-N]) / N
   ...:

In [4]: x = np.random.random(100000)

In [5]: N = 1000

In [6]: %timeit np.convolve(x, np.ones((N,))/N, mode='valid')
10 loops, best of 3: 172 ms per loop

In [7]: %timeit running_mean(x, N)
100 loops, best of 3: 6.72 ms per loop

In [8]: %timeit pd.rolling_mean(x, N)[N-1:]
100 loops, best of 3: 4.74 ms per loop

In [9]: np.allclose(pd.rolling_mean(x, N)[N-1:], running_mean(x, N))
Out[9]: True

关于如何处理边缘值,也有很好的选项。


或用于python计算的模块

在我在Tradewave.net的测试中,TA-lib总是赢:

import talib as ta
import numpy as np
import pandas as pd
import scipy
from scipy import signal
import time as t

PAIR = info.primary_pair
PERIOD = 30

def initialize():
    storage.reset()
    storage.elapsed = storage.get('elapsed', [0,0,0,0,0,0])

def cumsum_sma(array, period):
    ret = np.cumsum(array, dtype=float)
    ret[period:] = ret[period:] - ret[:-period]
    return ret[period - 1:] / period

def pandas_sma(array, period):
    return pd.rolling_mean(array, period)

def api_sma(array, period):
    # this method is native to Tradewave and does NOT return an array
    return (data[PAIR].ma(PERIOD))

def talib_sma(array, period):
    return ta.MA(array, period)

def convolve_sma(array, period):
    return np.convolve(array, np.ones((period,))/period, mode='valid')

def fftconvolve_sma(array, period):    
    return scipy.signal.fftconvolve(
        array, np.ones((period,))/period, mode='valid')    

def tick():

    close = data[PAIR].warmup_period('close')

    t1 = t.time()
    sma_api = api_sma(close, PERIOD)
    t2 = t.time()
    sma_cumsum = cumsum_sma(close, PERIOD)
    t3 = t.time()
    sma_pandas = pandas_sma(close, PERIOD)
    t4 = t.time()
    sma_talib = talib_sma(close, PERIOD)
    t5 = t.time()
    sma_convolve = convolve_sma(close, PERIOD)
    t6 = t.time()
    sma_fftconvolve = fftconvolve_sma(close, PERIOD)
    t7 = t.time()

    storage.elapsed[-1] = storage.elapsed[-1] + t2-t1
    storage.elapsed[-2] = storage.elapsed[-2] + t3-t2
    storage.elapsed[-3] = storage.elapsed[-3] + t4-t3
    storage.elapsed[-4] = storage.elapsed[-4] + t5-t4
    storage.elapsed[-5] = storage.elapsed[-5] + t6-t5    
    storage.elapsed[-6] = storage.elapsed[-6] + t7-t6        

    plot('sma_api', sma_api)  
    plot('sma_cumsum', sma_cumsum[-5])
    plot('sma_pandas', sma_pandas[-10])
    plot('sma_talib', sma_talib[-15])
    plot('sma_convolve', sma_convolve[-20])    
    plot('sma_fftconvolve', sma_fftconvolve[-25])

def stop():

    log('ticks....: %s' % info.max_ticks)

    log('api......: %.5f' % storage.elapsed[-1])
    log('cumsum...: %.5f' % storage.elapsed[-2])
    log('pandas...: %.5f' % storage.elapsed[-3])
    log('talib....: %.5f' % storage.elapsed[-4])
    log('convolve.: %.5f' % storage.elapsed[-5])    
    log('fft......: %.5f' % storage.elapsed[-6])

结果:

[2015-01-31 23:00:00] ticks....: 744
[2015-01-31 23:00:00] api......: 0.16445
[2015-01-31 23:00:00] cumsum...: 0.03189
[2015-01-31 23:00:00] pandas...: 0.03677
[2015-01-31 23:00:00] talib....: 0.00700  # <<< Winner!
[2015-01-31 23:00:00] convolve.: 0.04871
[2015-01-31 23:00:00] fft......: 0.22306


另一种不使用numpy或pandas找到移动平均线的方法

import itertools
sample = [2, 6, 10, 8, 11, 10]
list(itertools.starmap(
    lambda a,b: b/a, 
    enumerate(itertools.accumulate(sample), 1))
)

将打印[2.0,4.0,6.0,6.5,7.4,7.83333333333333333]

2.0 = (2)/1 4.0 is (2 + 6) / 2 6.0 = (2 + 6 + 10) / 3 .


有点晚了,但我已经做了我自己的小函数,它不环绕端点或垫与零,然后用于查找平均值。进一步的处理是,它还在线性间隔点上对信号进行重新采样。随意定制代码以获得其他特性。

该方法是一个简单的矩阵乘法与规范化高斯核。

def running_mean(y_in, x_in, N_out=101, sigma=1):
    '''
    Returns running mean as a Bell-curve weighted average at evenly spaced
    points. Does NOT wrap signal around, or pad with zeros.
    
    Arguments:
    y_in -- y values, the values to be smoothed and re-sampled
    x_in -- x values for array
    
    Keyword arguments:
    N_out -- NoOf elements in resampled array.
    sigma -- 'Width' of Bell-curve in units of param x .
    '''
    import numpy as np
    N_in = len(y_in)

    # Gaussian kernel
    x_out = np.linspace(np.min(x_in), np.max(x_in), N_out)
    x_in_mesh, x_out_mesh = np.meshgrid(x_in, x_out)
    gauss_kernel = np.exp(-np.square(x_in_mesh - x_out_mesh) / (2 * sigma**2))
    # Normalize kernel, such that the sum is one along axis 1
    normalization = np.tile(np.reshape(np.sum(gauss_kernel, axis=1), (N_out, 1)), (1, N_in))
    gauss_kernel_normalized = gauss_kernel / normalization
    # Perform running average as a linear operation
    y_out = gauss_kernel_normalized @ y_in

    return y_out, x_out

正弦信号加正态分布噪声的一个简单用法:


我知道这是一个老问题,但这里有一个解决方案,它不使用任何额外的数据结构或库。它在输入列表的元素数量上是线性的,我想不出任何其他方法来使它更有效(实际上,如果有人知道更好的分配结果的方法,请告诉我)。

注意:使用numpy数组而不是列表会快得多,但我想消除所有依赖关系。通过多线程执行也可以提高性能

该函数假设输入列表是一维的,所以要小心。

### Running mean/Moving average
def running_mean(l, N):
    sum = 0
    result = list( 0 for x in l)

    for i in range( 0, N ):
        sum = sum + l[i]
        result[i] = sum / (i+1)

    for i in range( N, len(l) ):
        sum = sum - l[i-N] + l[i]
        result[i] = sum / N

    return result

例子

假设我们有一个列表data =[1,2,3,4,5,6],我们想在它上面计算周期为3的滚动平均值,并且你还想要一个与输入列表相同大小的输出列表(这是最常见的情况)。

第一个元素的索引为0,因此滚动平均值应该在索引为-2、-1和0的元素上计算。显然,我们没有data[-2]和data[-1](除非您想使用特殊的边界条件),因此我们假设这些元素为0。这相当于对列表进行零填充,除了我们实际上不填充它,只是跟踪需要填充的索引(从0到N-1)。

所以,对于前N个元素,我们只是在累加器中不断地把元素加起来。

result[0] = (0 + 0 + 1) / 3  = 0.333    ==   (sum + 1) / 3
result[1] = (0 + 1 + 2) / 3  = 1        ==   (sum + 2) / 3
result[2] = (1 + 2 + 3) / 3  = 2        ==   (sum + 3) / 3

从元素N+1开始,简单的累加是行不通的。我们期望的结果是[3]=(2 + 3 + 4)/3 = 3,但这与(sum + 4)/3 = 3.333不同。

计算正确值的方法是用sum+4减去数据[0]= 1,从而得到sum+4 - 1 = 9。

这是因为目前sum =数据[0]+数据[1]+数据[2],但对于每个i >= N也是如此,因为在减法之前,sum是数据[i-N] +…+ data[i-2] + data[i-1]。


这个问题现在甚至比NeXuS上个月写的时候更古老,但我喜欢他的代码处理边缘情况的方式。然而,因为它是一个“简单移动平均”,它的结果滞后于它们应用的数据。我认为,通过对基于卷积()的方法应用类似的方法,可以以比NumPy的模式valid、same和full更令人满意的方式处理边缘情况。

我的贡献使用了一个中央运行平均值,以使其结果与他们的数据相一致。当可供使用的全尺寸窗口的点太少时,将从数组边缘的连续较小窗口计算运行平均值。[实际上,从连续较大的窗口,但这是一个实现细节。]

import numpy as np

def running_mean(l, N):
    # Also works for the(strictly invalid) cases when N is even.
    if (N//2)*2 == N:
        N = N - 1
    front = np.zeros(N//2)
    back = np.zeros(N//2)

    for i in range(1, (N//2)*2, 2):
        front[i//2] = np.convolve(l[:i], np.ones((i,))/i, mode = 'valid')
    for i in range(1, (N//2)*2, 2):
        back[i//2] = np.convolve(l[-i:], np.ones((i,))/i, mode = 'valid')
    return np.concatenate([front, np.convolve(l, np.ones((N,))/N, mode = 'valid'), back[::-1]])

它相对较慢,因为它使用了卷积(),并且可能会被真正的Pythonista修饰很多,但是,我相信这个想法是成立的。


你可以使用scipy. nmage .uniform_filter1d:

import numpy as np
from scipy.ndimage import uniform_filter1d
N = 1000
x = np.random.random(100000)
y = uniform_filter1d(x, size=N)

uniform_filter1d:

给出具有相同numpy形状的输出(即点数) 允许多种方式处理边界,其中'reflect'是默认的,但在我的情况下,我更想要'nearest'

它也相当快(比np快近50倍)。卷积,比上述cumsum方法快2-5倍):

%timeit y1 = np.convolve(x, np.ones((N,))/N, mode='same')
100 loops, best of 3: 9.28 ms per loop

%timeit y2 = uniform_filter1d(x, size=N)
10000 loops, best of 3: 191 µs per loop

这里有3个函数可以让你比较不同实现的错误/速度:

from __future__ import division
import numpy as np
import scipy.ndimage as ndi
def running_mean_convolve(x, N):
    return np.convolve(x, np.ones(N) / float(N), 'valid')
def running_mean_cumsum(x, N):
    cumsum = np.cumsum(np.insert(x, 0, 0))
    return (cumsum[N:] - cumsum[:-N]) / float(N)
def running_mean_uniform_filter1d(x, N):
    return ndi.uniform_filter1d(x, N, mode='constant', origin=-(N//2))[:-(N-1)]

对于一个简短、快速的解决方案,在一个循环中完成所有事情,没有依赖关系,下面的代码工作得很好。

mylist = [1, 2, 3, 4, 5, 6, 7]
N = 3
cumsum, moving_aves = [0], []

for i, x in enumerate(mylist, 1):
    cumsum.append(cumsum[i-1] + x)
    if i>=N:
        moving_ave = (cumsum[i] - cumsum[i-N])/N
        #can do stuff with moving_ave here
        moving_aves.append(moving_ave)

虽然这里有这个问题的解决方案,但请看看我的解决方案。这是非常简单和工作良好。

import numpy as np
dataset = np.asarray([1, 2, 3, 4, 5, 6, 7])
ma = list()
window = 3
for t in range(0, len(dataset)):
    if t+window <= len(dataset):
        indices = range(t, t+window)
        ma.append(np.average(np.take(dataset, indices)))
else:
    ma = np.asarray(ma)

仅使用Python标准库(内存高效)

只提供标准库deque的另一个版本。令我惊讶的是,大多数答案都使用pandas或numpy。

def moving_average(iterable, n=3):
    d = deque(maxlen=n)
    for i in iterable:
        d.append(i)
        if len(d) == n:
            yield sum(d)/n

r = moving_average([40, 30, 50, 46, 39, 44])
assert list(r) == [40.0, 42.0, 45.0, 43.0]

实际上,我在python文档中找到了另一个实现

def moving_average(iterable, n=3):
    # moving_average([40, 30, 50, 46, 39, 44]) --> 40.0 42.0 45.0 43.0
    # http://en.wikipedia.org/wiki/Moving_average
    it = iter(iterable)
    d = deque(itertools.islice(it, n-1))
    d.appendleft(0)
    s = sum(d)
    for elem in it:
        s += elem - d.popleft()
        d.append(elem)
        yield s / n

然而,在我看来,实现似乎比它应该的要复杂一些。但它肯定在标准python文档中是有原因的,有人能评论一下我的实现和标准文档吗?


从其他答案来看,我不认为这是问题所要求的,但我需要保持一个不断增长的值列表的运行平均值。

因此,如果你想保持从某个地方(站点,测量设备等)获取的值的列表和最近n个值更新的平均值,你可以使用下面的代码,这将最大限度地减少添加新元素的工作:

class Running_Average(object):
    def __init__(self, buffer_size=10):
        """
        Create a new Running_Average object.

        This object allows the efficient calculation of the average of the last
        `buffer_size` numbers added to it.

        Examples
        --------
        >>> a = Running_Average(2)
        >>> a.add(1)
        >>> a.get()
        1.0
        >>> a.add(1)  # there are two 1 in buffer
        >>> a.get()
        1.0
        >>> a.add(2)  # there's a 1 and a 2 in the buffer
        >>> a.get()
        1.5
        >>> a.add(2)
        >>> a.get()  # now there's only two 2 in the buffer
        2.0
        """
        self._buffer_size = int(buffer_size)  # make sure it's an int
        self.reset()

    def add(self, new):
        """
        Add a new number to the buffer, or replaces the oldest one there.
        """
        new = float(new)  # make sure it's a float
        n = len(self._buffer)
        if n < self.buffer_size:  # still have to had numbers to the buffer.
            self._buffer.append(new)
            if self._average != self._average:  # ~ if isNaN().
                self._average = new  # no previous numbers, so it's new.
            else:
                self._average *= n  # so it's only the sum of numbers.
                self._average += new  # add new number.
                self._average /= (n+1)  # divide by new number of numbers.
        else:  # buffer full, replace oldest value.
            old = self._buffer[self._index]  # the previous oldest number.
            self._buffer[self._index] = new  # replace with new one.
            self._index += 1  # update the index and make sure it's...
            self._index %= self.buffer_size  # ... smaller than buffer_size.
            self._average -= old/self.buffer_size  # remove old one...
            self._average += new/self.buffer_size  # ...and add new one...
            # ... weighted by the number of elements.

    def __call__(self):
        """
        Return the moving average value, for the lazy ones who don't want
        to write .get .
        """
        return self._average

    def get(self):
        """
        Return the moving average value.
        """
        return self()

    def reset(self):
        """
        Reset the moving average.

        If for some reason you don't want to just create a new one.
        """
        self._buffer = []  # could use np.empty(self.buffer_size)...
        self._index = 0  # and use this to keep track of how many numbers.
        self._average = float('nan')  # could use np.NaN .

    def get_buffer_size(self):
        """
        Return current buffer_size.
        """
        return self._buffer_size

    def set_buffer_size(self, buffer_size):
        """
        >>> a = Running_Average(10)
        >>> for i in range(15):
        ...     a.add(i)
        ...
        >>> a()
        9.5
        >>> a._buffer  # should not access this!!
        [10.0, 11.0, 12.0, 13.0, 14.0, 5.0, 6.0, 7.0, 8.0, 9.0]

        Decreasing buffer size:
        >>> a.buffer_size = 6
        >>> a._buffer  # should not access this!!
        [9.0, 10.0, 11.0, 12.0, 13.0, 14.0]
        >>> a.buffer_size = 2
        >>> a._buffer
        [13.0, 14.0]

        Increasing buffer size:
        >>> a.buffer_size = 5
        Warning: no older data available!
        >>> a._buffer
        [13.0, 14.0]

        Keeping buffer size:
        >>> a = Running_Average(10)
        >>> for i in range(15):
        ...     a.add(i)
        ...
        >>> a()
        9.5
        >>> a._buffer  # should not access this!!
        [10.0, 11.0, 12.0, 13.0, 14.0, 5.0, 6.0, 7.0, 8.0, 9.0]
        >>> a.buffer_size = 10  # reorders buffer!
        >>> a._buffer
        [5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0, 14.0]
        """
        buffer_size = int(buffer_size)
        # order the buffer so index is zero again:
        new_buffer = self._buffer[self._index:]
        new_buffer.extend(self._buffer[:self._index])
        self._index = 0
        if self._buffer_size < buffer_size:
            print('Warning: no older data available!')  # should use Warnings!
        else:
            diff = self._buffer_size - buffer_size
            print(diff)
            new_buffer = new_buffer[diff:]
        self._buffer_size = buffer_size
        self._buffer = new_buffer

    buffer_size = property(get_buffer_size, set_buffer_size)

你可以测试它,例如:

def graph_test(N=200):
    import matplotlib.pyplot as plt
    values = list(range(N))
    values_average_calculator = Running_Average(N/2)
    values_averages = []
    for value in values:
        values_average_calculator.add(value)
        values_averages.append(values_average_calculator())
    fig, ax = plt.subplots(1, 1)
    ax.plot(values, label='values')
    ax.plot(values_averages, label='averages')
    ax.grid()
    ax.set_xlim(0, N)
    ax.set_ylim(0, N)
    fig.show()

这使:


比起numpy或scipy,我建议熊猫们更快地做到这一点:

df['data'].rolling(3).mean()

这取列“数据”的3个周期的移动平均值(MA)。你也可以计算移位的版本,例如排除当前单元格的版本(向后移位一个)可以很容易地计算为:

df['data'].shift(periods=1).rolling(3).mean()

移动平均过滤器怎么样?它也是一个单行程序,它的优点是,如果你需要矩形以外的东西,你可以很容易地操作窗口类型。一个n长的简单移动平均数组a:

lfilter(np.ones(N)/N, [1], a)[N:]

应用三角形窗口后:

lfilter(np.ones(N)*scipy.signal.triang(N)/N, [1], a)[N:]

注:我通常会在最后丢弃前N个样本作为假的,因此[N:],但这是没有必要的,只是个人选择的问题。


上面有很多关于计算运行平均值的答案。我的回答增加了两个额外的特征:

忽略nan值 计算N个相邻值的平均值,不包括兴趣值本身

这第二个特征对于确定哪些值与总体趋势有一定的差异特别有用。

我使用numpy。cumsum,因为这是最省时的方法(参见上面Alleo的回答)。

N=10 # number of points to test on each side of point of interest, best if even
padded_x = np.insert(np.insert( np.insert(x, len(x), np.empty(int(N/2))*np.nan), 0, np.empty(int(N/2))*np.nan ),0,0)
n_nan = np.cumsum(np.isnan(padded_x))
cumsum = np.nancumsum(padded_x) 
window_sum = cumsum[N+1:] - cumsum[:-(N+1)] - x # subtract value of interest from sum of all values within window
window_n_nan = n_nan[N+1:] - n_nan[:-(N+1)] - np.isnan(x)
window_n_values = (N - window_n_nan)
movavg = (window_sum) / (window_n_values)

这段代码只适用于偶数n。它可以通过改变np来调整奇数。插入padded_x和n_nan。

输出示例(黑色为raw,蓝色为movavg):

这段代码可以很容易地修改,以删除从小于cutoff = 3的非nan值计算的所有移动平均值。

window_n_values = (N - window_n_nan).astype(float) # dtype must be float to set some values to nan
cutoff = 3
window_n_values[window_n_values<cutoff] = np.nan
movavg = (window_sum) / (window_n_values)


上面的一个答案中有一个mab的注释,它有这个方法。瓶颈有move_mean,这是一个简单的移动平均:

import numpy as np
import bottleneck as bn

a = np.arange(10) + np.random.random(10)

mva = bn.move_mean(a, window=2, min_count=1)

Min_count是一个很方便的参数,它可以取数组中该点的移动平均值。如果你不设置min_count,它将等于window,并且直到window points的所有内容都将是nan。


另一个解决方案是使用标准库和deque:

from collections import deque
import itertools

def moving_average(iterable, n=3):
    # http://en.wikipedia.org/wiki/Moving_average
    it = iter(iterable) 
    # create an iterable object from input argument
    d = deque(itertools.islice(it, n-1))  
    # create deque object by slicing iterable
    d.appendleft(0)
    s = sum(d)
    for elem in it:
        s += elem - d.popleft()
        d.append(elem)
        yield s / n

# example on how to use it
for i in  moving_average([40, 30, 50, 46, 39, 44]):
    print(i)

# 40.0
# 42.0
# 45.0
# 43.0

出于教学目的,让我再添加两个Numpy解决方案(比cumsum解决方案慢):

import numpy as np
from numpy.lib.stride_tricks import as_strided

def ra_strides(arr, window):
    ''' Running average using as_strided'''
    n = arr.shape[0] - window + 1
    arr_strided = as_strided(arr, shape=[n, window], strides=2*arr.strides)
    return arr_strided.mean(axis=1)

def ra_add(arr, window):
    ''' Running average using add.reduceat'''
    n = arr.shape[0] - window + 1
    indices = np.array([0, window]*n) + np.repeat(np.arange(n), 2)
    arr = np.append(arr, 0)
    return np.add.reduceat(arr, indices )[::2]/window

使用的函数:as_strided, add.reduceat


Python标准库解决方案

这个生成器函数接受一个可迭代对象和一个窗口大小为N的值,并生成窗口内当前值的平均值。它使用了deque,这是一种类似于列表的数据结构,但针对在两端进行快速修改(弹出、追加)进行了优化。

from collections import deque
from itertools import islice

def sliding_avg(iterable, N):        
    it = iter(iterable)
    window = deque(islice(it, N))        
    num_vals = len(window)

    if num_vals < N:
        msg = 'window size {} exceeds total number of values {}'
        raise ValueError(msg.format(N, num_vals))

    N = float(N) # force floating point division if using Python 2
    s = sum(window)
    
    while True:
        yield s/N
        try:
            nxt = next(it)
        except StopIteration:
            break
        s = s - window.popleft() + nxt
        window.append(nxt)
        

下面是函数的运行情况:

>>> values = range(100)
>>> N = 5
>>> window_avg = sliding_avg(values, N)
>>> 
>>> next(window_avg) # (0 + 1 + 2 + 3 + 4)/5
>>> 2.0
>>> next(window_avg) # (1 + 2 + 3 + 4 + 5)/5
>>> 3.0
>>> next(window_avg) # (2 + 3 + 4 + 5 + 6)/5
>>> 4.0

我觉得使用瓶颈可以很好地解决这个问题

参见下面的基本示例:

import numpy as np
import bottleneck as bn

a = np.random.randint(4, 1000, size=100)
mm = bn.move_mean(a, window=5, min_count=1)

“mm”是“a”的移动平均值。 “窗口”是考虑移动均值的最大条目数。 "min_count"是考虑移动平均值的最小条目数(例如,对于前几个元素或如果数组有nan值)。

好在瓶颈有助于处理nan值,而且非常高效。


使用@Aikude的变量,我编写了一行程序。

import numpy as np

mylist = [1, 2, 3, 4, 5, 6, 7]
N = 3

mean = [np.mean(mylist[x:x+N]) for x in range(len(mylist)-N+1)]
print(mean)

>>> [2.0, 3.0, 4.0, 5.0, 6.0]

上述所有的解决方案都很差,因为它们缺乏

由于本机python而不是numpy向量化实现, 数值稳定性,由于numpy使用不当。cumsum或 由于O(len(x) * w)实现为卷积的速度。

鉴于

import numpy
m = 10000
x = numpy.random.rand(m)
w = 1000

注意x_[:w].sum()等于x[:w-1].sum()。因此,对于第一个平均值,numpy.cumsum(…)加上x[w] / w(通过x_[w+1] / w),并减去0(从x_[0] / w)。结果是x[0:w].mean()

通过cumsum,您将通过添加x[w+1] / w并减去x[0] / w来更新第二个平均值,从而得到x[1:w+1].mean()。

这将一直进行,直到到达x[-w:].mean()。

x_ = numpy.insert(x, 0, 0)
sliding_average = x_[:w].sum() / w + numpy.cumsum(x_[w:] - x_[:-w]) / w

这个解是向量化的,O(m),可读且数值稳定。


一个新的卷积配方被合并到Python 3.10中。

鉴于


import collections, operator

from itertools import chain, repeat


size = 3 + 1
kernel = [1/size] * size                                              

Code

def convolve(signal, kernel):
    # See:  https://betterexplained.com/articles/intuitive-convolution/
    # convolve(data, [0.25, 0.25, 0.25, 0.25]) --> Moving average (blur)
    # convolve(data, [1, -1]) --> 1st finite difference (1st derivative)
    # convolve(data, [1, -2, 1]) --> 2nd finite difference (2nd derivative)
    kernel = list(reversed(kernel))
    n = len(kernel)
    window = collections.deque([0] * n, maxlen=n)
    for x in chain(signal, repeat(0, n-1)):
        window.append(x)
        yield sum(map(operator.mul, kernel, window))

Demo

list(convolve(range(1, 6), kernel))
# [0.25, 0.75, 1.5, 2.5, 3.5, 3.0, 2.25, 1.25]

细节

卷积是一种可以应用于移动平均的一般数学运算。其思想是,给定一些数据,您将数据子集(窗口)作为“掩码”或“内核”在数据中滑动,在每个窗口上执行特定的数学操作。在移动平均的情况下,核是平均值:

现在可以通过more_itertools.convolve使用这个实现。 More_itertools是一个流行的第三方包;通过> PIP Install more_itertools安装。


如果你必须为非常小的数组(少于200个元素)重复这样做,我发现只用线性代数就能得到最快的结果。 最慢的部分是建立你的乘法矩阵y,你只需要做一次,但之后可能会更快。

import numpy as np
import random 

N = 100      # window size
size =200     # array length

x = np.random.random(size)
y = np.eye(size, dtype=float)

# prepare matrix
for i in range(size):
  y[i,i:i+N] = 1./N
  
# calculate running mean
z = np.inner(x,y.T)[N-1:]


我的解决方案是基于维基百科上的“简单移动平均”。

from numba import jit
@jit
def sma(x, N):
    s = np.zeros_like(x)
    k = 1 / N
    s[0] = x[0] * k
    for i in range(1, N + 1):
        s[i] = s[i - 1] + x[i] * k
    for i in range(N, x.shape[0]):
        s[i] = s[i - 1] + (x[i] - x[i - N]) * k
    s = s[N - 1:]
    return s

与之前建议的解决方案相比,它比scipy最快的解决方案“uniform_filter1d”快两倍,并且具有相同的错误顺序。 速度测试:

import numpy as np    
x = np.random.random(10000000)
N = 1000

from scipy.ndimage.filters import uniform_filter1d
%timeit uniform_filter1d(x, size=N)
95.7 ms ± 9.34 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
%timeit sma(x, N)
47.3 ms ± 3.42 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

错误的比较:

np.max(np.abs(np.convolve(x, np.ones((N,))/N, mode='valid') - uniform_filter1d(x, size=N, mode='constant', origin=-(N//2))[:-(N-1)]))
8.604228440844963e-14
np.max(np.abs(np.convolve(x, np.ones((N,))/N, mode='valid') - sma(x, N)))
1.41886502547095e-13