'''using scipy signal and numpy correlate to calculate some time series
statistics
original developer notes
see also scikits.timeseries (movstat is partially inspired by it)
added 2009-08-29
timeseries moving stats are in c, autocorrelation similar to here
I thought I saw moving stats somewhere in python, maybe not)
TODO
moving statistics
- filters don't handle boundary conditions nicely (correctly ?)
e.g. minimum order filter uses 0 for out of bounds value
-> append and prepend with last resp. first value
- enhance for nd arrays, with axis = 0
Note: Equivalence for 1D signals
>>> np.all(signal.correlate(x,[1,1,1],'valid')==np.correlate(x,[1,1,1]))
True
>>> np.all(ndimage.filters.correlate(x,[1,1,1], origin = -1)[:-3+1]==np.correlate(x,[1,1,1]))
True
# multidimensional, but, it looks like it uses common filter across time series, no VAR
ndimage.filters.correlate(np.vstack([x,x]),np.array([[1,1,1],[0,0,0]]), origin = 1)
ndimage.filters.correlate(x,[1,1,1],origin = 1))
ndimage.filters.correlate(np.vstack([x,x]),np.array([[0.5,0.5,0.5],[0.5,0.5,0.5]]), \
origin = 1)
>>> np.all(ndimage.filters.correlate(np.vstack([x,x]),np.array([[1,1,1],[0,0,0]]), origin = 1)[0]==\
ndimage.filters.correlate(x,[1,1,1],origin = 1))
True
>>> np.all(ndimage.filters.correlate(np.vstack([x,x]),np.array([[0.5,0.5,0.5],[0.5,0.5,0.5]]), \
origin = 1)[0]==ndimage.filters.correlate(x,[1,1,1],origin = 1))
update
2009-09-06: cosmetic changes, rearrangements
'''
from __future__ import print_function
import numpy as np
from scipy import signal
from numpy.testing import assert_array_equal, assert_array_almost_equal
def expandarr(x,k):
#make it work for 2D or nD with axis
kadd = k
if np.ndim(x) == 2:
kadd = (kadd, np.shape(x)[1])
return np.r_[np.ones(kadd)*x[0],x,np.ones(kadd)*x[-1]]
[docs]def movorder(x, order = 'med', windsize=3, lag='lagged'):
'''moving order statistics
Parameters
----------
x : array
time series data
order : float or 'med', 'min', 'max'
which order statistic to calculate
windsize : int
window size
lag : 'lagged', 'centered', or 'leading'
location of window relative to current position
Returns
-------
filtered array
'''
#if windsize is even should it raise ValueError
if lag == 'lagged':
lead = windsize//2
elif lag == 'centered':
lead = 0
elif lag == 'leading':
lead = -windsize//2 +1
else:
raise ValueError
if np.isfinite(order): #if np.isnumber(order):
ord = order # note: ord is a builtin function
elif order == 'med':
ord = (windsize - 1)/2
elif order == 'min':
ord = 0
elif order == 'max':
ord = windsize - 1
else:
raise ValueError
#return signal.order_filter(x,np.ones(windsize),ord)[:-lead]
xext = expandarr(x, windsize)
#np.r_[np.ones(windsize)*x[0],x,np.ones(windsize)*x[-1]]
return signal.order_filter(xext,np.ones(windsize),ord)[windsize-lead:-(windsize+lead)]
def check_movorder():
'''graphical test for movorder'''
import matplotlib.pylab as plt
x = np.arange(1,10)
xo = movorder(x, order='max')
assert_array_equal(xo, x)
x = np.arange(10,1,-1)
xo = movorder(x, order='min')
assert_array_equal(xo, x)
assert_array_equal(movorder(x, order='min', lag='centered')[:-1], x[1:])
tt = np.linspace(0,2*np.pi,15)
x = np.sin(tt) + 1
xo = movorder(x, order='max')
plt.figure()
plt.plot(tt,x,'.-',tt,xo,'.-')
plt.title('moving max lagged')
xo = movorder(x, order='max', lag='centered')
plt.figure()
plt.plot(tt,x,'.-',tt,xo,'.-')
plt.title('moving max centered')
xo = movorder(x, order='max', lag='leading')
plt.figure()
plt.plot(tt,x,'.-',tt,xo,'.-')
plt.title('moving max leading')
# identity filter
##>>> signal.order_filter(x,np.ones(1),0)
##array([ 1., 2., 3., 4., 5., 6., 7., 8., 9.])
# median filter
##signal.medfilt(np.sin(x), kernel_size=3)
##>>> plt.figure()
##<matplotlib.figure.Figure object at 0x069BBB50>
##>>> x=np.linspace(0,3,100);plt.plot(x,np.sin(x),x,signal.medfilt(np.sin(x), kernel_size=3))
# remove old version
##def movmeanvar(x, windowsize=3, valid='same'):
## '''
## this should also work along axis or at least for columns
## '''
## n = x.shape[0]
## x = expandarr(x, windowsize - 1)
## takeslice = slice(windowsize-1, n + windowsize-1)
## avgkern = (np.ones(windowsize)/float(windowsize))
## m = np.correlate(x, avgkern, 'same')#[takeslice]
## print(m.shape)
## print(x.shape)
## xm = x - m
## v = np.correlate(x*x, avgkern, 'same') - m**2
## v1 = np.correlate(xm*xm, avgkern, valid) #not correct for var of window
###>>> np.correlate(xm*xm,np.array([1,1,1])/3.0,'valid')-np.correlate(xm*xm,np.array([1,1,1])/3.0,'valid')**2
## return m[takeslice], v[takeslice], v1
[docs]def movmean(x, windowsize=3, lag='lagged'):
'''moving window mean
Parameters
----------
x : array
time series data
windsize : int
window size
lag : 'lagged', 'centered', or 'leading'
location of window relative to current position
Returns
-------
mk : array
moving mean, with same shape as x
Notes
-----
for leading and lagging the data array x is extended by the closest value of the array
'''
return movmoment(x, 1, windowsize=windowsize, lag=lag)
[docs]def movvar(x, windowsize=3, lag='lagged'):
'''moving window variance
Parameters
----------
x : array
time series data
windsize : int
window size
lag : 'lagged', 'centered', or 'leading'
location of window relative to current position
Returns
-------
mk : array
moving variance, with same shape as x
'''
m1 = movmoment(x, 1, windowsize=windowsize, lag=lag)
m2 = movmoment(x, 2, windowsize=windowsize, lag=lag)
return m2 - m1*m1
[docs]def movmoment(x, k, windowsize=3, lag='lagged'):
'''non-central moment
Parameters
----------
x : array
time series data
windsize : int
window size
lag : 'lagged', 'centered', or 'leading'
location of window relative to current position
Returns
-------
mk : array
k-th moving non-central moment, with same shape as x
Notes
-----
If data x is 2d, then moving moment is calculated for each
column.
'''
windsize = windowsize
#if windsize is even should it raise ValueError
if lag == 'lagged':
#lead = -0 + windsize #windsize//2
lead = -0# + (windsize-1) + windsize//2
sl = slice((windsize-1) or None, -2*(windsize-1) or None)
elif lag == 'centered':
lead = -windsize//2 #0#-1 #+ #(windsize-1)
sl = slice((windsize-1)+windsize//2 or None, -(windsize-1)-windsize//2 or None)
elif lag == 'leading':
#lead = -windsize +1#+1 #+ (windsize-1)#//2 +1
lead = -windsize +2 #-windsize//2 +1
sl = slice(2*(windsize-1)+1+lead or None, -(2*(windsize-1)+lead)+1 or None)
else:
raise ValueError
avgkern = (np.ones(windowsize)/float(windowsize))
xext = expandarr(x, windsize-1)
#Note: expandarr increases the array size by 2*(windsize-1)
#sl = slice(2*(windsize-1)+1+lead or None, -(2*(windsize-1)+lead)+1 or None)
print(sl)
if xext.ndim == 1:
return np.correlate(xext**k, avgkern, 'full')[sl]
#return np.correlate(xext**k, avgkern, 'same')[windsize-lead:-(windsize+lead)]
else:
print(xext.shape)
print(avgkern[:,None].shape)
# try first with 2d along columns, possibly ndim with axis
return signal.correlate(xext**k, avgkern[:,None], 'full')[sl,:]
#x=0.5**np.arange(10);xm=x-x.mean();a=np.correlate(xm,[1],'full')
#x=0.5**np.arange(3);np.correlate(x,x,'same')
##>>> x=0.5**np.arange(10);xm=x-x.mean();a=np.correlate(xm,xo,'full')
##
##>>> xo=np.ones(10);d=np.correlate(xo,xo,'full')
##>>> xo
##xo=np.ones(10);d=np.correlate(xo,xo,'full')
##>>> x=np.ones(10);xo=x-x.mean();a=np.correlate(xo,xo,'full')
##>>> xo=np.ones(10);d=np.correlate(xo,xo,'full')
##>>> d
##array([ 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 9.,
## 8., 7., 6., 5., 4., 3., 2., 1.])
##def ccovf():
## pass
## #x=0.5**np.arange(10);xm=x-x.mean();a=np.correlate(xm,xo,'full')
__all__ = ['movorder', 'movmean', 'movvar', 'movmoment']
if __name__ == '__main__':
print('\ncheckin moving mean and variance')
nobs = 10
x = np.arange(nobs)
ws = 3
ave = np.array([ 0., 1/3., 1., 2., 3., 4., 5., 6., 7., 8.,
26/3., 9])
va = np.array([[ 0. , 0. ],
[ 0.22222222, 0.88888889],
[ 0.66666667, 2.66666667],
[ 0.66666667, 2.66666667],
[ 0.66666667, 2.66666667],
[ 0.66666667, 2.66666667],
[ 0.66666667, 2.66666667],
[ 0.66666667, 2.66666667],
[ 0.66666667, 2.66666667],
[ 0.66666667, 2.66666667],
[ 0.22222222, 0.88888889],
[ 0. , 0. ]])
ave2d = np.c_[ave, 2*ave]
print(movmean(x, windowsize=ws, lag='lagged'))
print(movvar(x, windowsize=ws, lag='lagged'))
print([np.var(x[i-ws:i]) for i in range(ws, nobs)])
m1 = movmoment(x, 1, windowsize=3, lag='lagged')
m2 = movmoment(x, 2, windowsize=3, lag='lagged')
print(m1)
print(m2)
print(m2 - m1*m1)
# this implicitly also tests moment
assert_array_almost_equal(va[ws-1:,0],
movvar(x, windowsize=3, lag='leading'))
assert_array_almost_equal(va[ws//2:-ws//2+1,0],
movvar(x, windowsize=3, lag='centered'))
assert_array_almost_equal(va[:-ws+1,0],
movvar(x, windowsize=ws, lag='lagged'))
print('\nchecking moving moment for 2d (columns only)')
x2d = np.c_[x, 2*x]
print(movmoment(x2d, 1, windowsize=3, lag='centered'))
print(movmean(x2d, windowsize=ws, lag='lagged'))
print(movvar(x2d, windowsize=ws, lag='lagged'))
assert_array_almost_equal(va[ws-1:,:],
movvar(x2d, windowsize=3, lag='leading'))
assert_array_almost_equal(va[ws//2:-ws//2+1,:],
movvar(x2d, windowsize=3, lag='centered'))
assert_array_almost_equal(va[:-ws+1,:],
movvar(x2d, windowsize=ws, lag='lagged'))
assert_array_almost_equal(ave2d[ws-1:],
movmoment(x2d, 1, windowsize=3, lag='leading'))
assert_array_almost_equal(ave2d[ws//2:-ws//2+1],
movmoment(x2d, 1, windowsize=3, lag='centered'))
assert_array_almost_equal(ave2d[:-ws+1],
movmean(x2d, windowsize=ws, lag='lagged'))
from scipy import ndimage
print(ndimage.filters.correlate1d(x2d, np.array([1,1,1])/3., axis=0))
#regression test check
xg = np.array([ 0. , 0.1, 0.3, 0.6, 1. , 1.5, 2.1, 2.8, 3.6,
4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5, 11.5, 12.5,
13.5, 14.5, 15.5, 16.5, 17.5, 18.5, 19.5, 20.5, 21.5,
22.5, 23.5, 24.5, 25.5, 26.5, 27.5, 28.5, 29.5, 30.5,
31.5, 32.5, 33.5, 34.5, 35.5, 36.5, 37.5, 38.5, 39.5,
40.5, 41.5, 42.5, 43.5, 44.5, 45.5, 46.5, 47.5, 48.5,
49.5, 50.5, 51.5, 52.5, 53.5, 54.5, 55.5, 56.5, 57.5,
58.5, 59.5, 60.5, 61.5, 62.5, 63.5, 64.5, 65.5, 66.5,
67.5, 68.5, 69.5, 70.5, 71.5, 72.5, 73.5, 74.5, 75.5,
76.5, 77.5, 78.5, 79.5, 80.5, 81.5, 82.5, 83.5, 84.5,
85.5, 86.5, 87.5, 88.5, 89.5, 90.5, 91.5, 92.5, 93.5,
94.5])
assert_array_almost_equal(xg, movmean(np.arange(100), 10,'lagged'))
xd = np.array([ 0.3, 0.6, 1. , 1.5, 2.1, 2.8, 3.6, 4.5, 5.5,
6.5, 7.5, 8.5, 9.5, 10.5, 11.5, 12.5, 13.5, 14.5,
15.5, 16.5, 17.5, 18.5, 19.5, 20.5, 21.5, 22.5, 23.5,
24.5, 25.5, 26.5, 27.5, 28.5, 29.5, 30.5, 31.5, 32.5,
33.5, 34.5, 35.5, 36.5, 37.5, 38.5, 39.5, 40.5, 41.5,
42.5, 43.5, 44.5, 45.5, 46.5, 47.5, 48.5, 49.5, 50.5,
51.5, 52.5, 53.5, 54.5, 55.5, 56.5, 57.5, 58.5, 59.5,
60.5, 61.5, 62.5, 63.5, 64.5, 65.5, 66.5, 67.5, 68.5,
69.5, 70.5, 71.5, 72.5, 73.5, 74.5, 75.5, 76.5, 77.5,
78.5, 79.5, 80.5, 81.5, 82.5, 83.5, 84.5, 85.5, 86.5,
87.5, 88.5, 89.5, 90.5, 91.5, 92.5, 93.5, 94.5, 95.4,
96.2, 96.9, 97.5, 98. , 98.4, 98.7, 98.9, 99. ])
assert_array_almost_equal(xd, movmean(np.arange(100), 10,'leading'))
xc = np.array([ 1.36363636, 1.90909091, 2.54545455, 3.27272727,
4.09090909, 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. ,
36. , 37. , 38. , 39. ,
40. , 41. , 42. , 43. ,
44. , 45. , 46. , 47. ,
48. , 49. , 50. , 51. ,
52. , 53. , 54. , 55. ,
56. , 57. , 58. , 59. ,
60. , 61. , 62. , 63. ,
64. , 65. , 66. , 67. ,
68. , 69. , 70. , 71. ,
72. , 73. , 74. , 75. ,
76. , 77. , 78. , 79. ,
80. , 81. , 82. , 83. ,
84. , 85. , 86. , 87. ,
88. , 89. , 90. , 91. ,
92. , 93. , 94. , 94.90909091,
95.72727273, 96.45454545, 97.09090909, 97.63636364])
assert_array_almost_equal(xc, movmean(np.arange(100), 11,'centered'))
