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annotate allan.py @ 4:9d016a2a2702

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Fix setup.py
author Daniele Nicolodi <daniele@grinta.net>
date Tue, 24 Mar 2015 18:32:11 +0100
parents ff2192f47448
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Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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1 import numpy as np
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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2 from scipy import polyfit, polyval
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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3 import matplotlib.pyplot as plt
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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4 import numexpr
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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5
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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6 __all__ = ['outliers', 'detrend', 'fastdetrend',
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7 'adev', 'xadev', 'xmdev', 'xtdev', 'xavar', 'xmvar', 'tau' ]
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9
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10 def outliers(y, alpha=6, remove=False):
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11 """Detect and optionally remove outliers"""
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12
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13 m = np.mean(y)
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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14 v = np.var(y)
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15
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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16 outliers = np.abs(y - m) > (alpha * np.sqrt(v))
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17
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18 if remove:
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19 x = lambda z: z.nonzero()[0]
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20 y[outliers] = np.interp(x(outliers), x(~outliers), y[~outliers])
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21
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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22 return np.nonzero(outliers)[0]
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23
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24
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25 def detrend(y, order=1):
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26 """Detrend"""
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27
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28 x = np.arange(y.size)
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29 p = polyfit(x, y, order)
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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30 y = y - polyval(p, x)
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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31 return y
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32
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33
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34 def fastdetrend(y, order=1, downsample=1000):
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35 # time base
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36 x = np.arange(y.size)
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37 # compute detrend polynomial from downsampled data
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38 p = polyfit(x[::downsample], y[::downsample], order)
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39
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40 # construct numexpr expression
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41 expr = []
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42 args = {'y': y, 'x': x}
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43 for i in range(order + 1):
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44 expr.append("p%d" % i + "*x" * i)
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45 args["p%d" % i] = p[order - i]
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46 expr = "y - (%s)" % " + ".join(expr)
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47
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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48 # evaluate expression
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49 y = numexpr.evaluate(expr, local_dict=args)
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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50 return y
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51
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52
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53 def tau(expmin=0, expmax=4):
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54 return np.ravel(np.power(10, np.arange(expmin, expmax))[:,np.newaxis] * np.arange(0, 10))
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55
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56
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57 def tau124(expmin=0, expmax=4):
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58 return np.ravel(np.power(10.0, np.arange(expmin, expmax))[:,np.newaxis] * np.array([1, 2, 4]))
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59
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60
0
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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61 def adev(x, tau, sampl=1.0):
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62 """Allan deviation"""
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63
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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64 x = np.asarray(x)
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65 tau = np.asarray(tau)
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66
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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67 # allocate output vectors
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68 adev = np.zeros(tau.size)
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69 dadev = np.zeros(tau.size)
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70
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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71 # samples
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72 n = x.size
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73 # partitioning
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74 p = np.floor(tau * sampl).astype(int)
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75
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76 for i, m in enumerate(p):
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77 d = x[0:n - n % m].reshape(-1, m)
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78 y = np.mean(d, axis=1)
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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79 adev[i] = np.sqrt(0.5 * np.mean(np.diff(y)**2))
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80 dadev[i] = adev[i] / np.sqrt(y.size)
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81
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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82 return adev, dadev
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83
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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84
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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85 from _allan import _xmvar, _xmvar2, _xavar
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86
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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87 # Functions to compute Allan deviation and modified Allan deviation
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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88 # from time error data. For an oscillator described by the equation
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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89 # v(t) = v0 * cos(2*pi * f0 * t + phi(t)) where f0 is the nominal
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90 # oscillator frequency the time deviation is computed as: x(t) =
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91 # phi(t) / (2*pi * f0)
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92 #
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93 # The Symmetricom 5115A phase analyzer outputs data in units of cycles
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94 # of the input signal. To obtain time deviation from the data stream
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95 # d(t) it is sufficient to compute: x(t) = d(t) / f0 where f0 is the
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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96 # nominal frequency of the oscillator under test
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97
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98 def xmvar0(x, tau, tau0=1.0):
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99
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100 x = np.asarray(x)
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101 tau = np.asarray(tau)
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102
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103 # allocate output vectors
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104 mvar = np.zeros(tau.size)
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105
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106 # partitioning
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107 p = (tau // tau0).astype(int)
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108
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109 for k, m in enumerate(p):
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110 mvar[k] = _xmvar(x, m)
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111 # c = 0
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112 # for j in xrange(x.size - 3 * m + 1):
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113 # v = 0
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114 # for i in xrange(j, j + m):
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115 # v += (x[i + 2 * m] - 2 * x[i + m] + x[i]) / m
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116 # c += v*v
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117 # mavar[k] = c / (2.0 * m*m * (n - 3 * m + 1))
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118
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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119 return np.sqrt(mvar) / tau0
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120
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121
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122 def xmvar(x, tau, tau0=1.0):
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123
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124 x = np.asarray(x)
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125 tau = np.asarray(tau)
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126
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127 # partitioning
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128 p = (tau // tau0).astype(int)
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129
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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130 return _xmvar2(x, p) / (tau0 * tau0)
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131
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132
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133 def xmdev(x, tau, tau0=1.0):
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134
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135 return np.sqrt(xmvar(x, tau, tau0))
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136
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137
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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138 def xtdev(x, tau, tau0=1.0):
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139
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140 return np.sqrt(xmvar(x, tau, tau0)) * tau / np.sqrt(3.0)
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141
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142
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143 def xavar(x, tau, tau0=1.0):
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144
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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145 x = np.asarray(x)
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146 tau = np.asarray(tau)
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147
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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148 # partitioning
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149 p = (tau // tau0).astype(np.int32)
0
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150
Daniele Nicolodi <daniele.nicolodi@obspm.fr>
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151 return _xavar(x, p) / (tau0 * tau0)
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152
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153
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154 def xadev(x, tau, tau0=1.0):
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155 return np.sqrt(xavar(x, tau, tau0))