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?
当前回答
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()
其他回答
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。
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:
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。
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)
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:]
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