Tagallantools

AllanTools 2018.03 now LGPL

By popular demand, AllanTools 2018.03 is now released under LGPL license.

Get it at: PyPi or github.

Work with integrating noise-identification with downstream confidence-interval estimation and bias correction continues as time permits.

Power Law Noise Identification for AllanTools

For AllanTools statistics both bias-correction and confidence interval calculation requires identifying the dominant power law noise in the input time-series.

The usual noise-types studied have phase PSD noise-slopes "b" ranging from 0 to -4 (or even -5 or -6), corresponding to frequency PSD noise-slopes "a" ranging from +2 to -2 (where a=b+2). These 'colors of noise' can be visualized like this:

 

Four colors of noise. Note frequency PSD slope "a" related to phase PSD slobe "b" by a=b+2. Lower graphs show tau-slopes "mu" for ADEV and MDEV. Data point colors don't match with figures below - sorry.

I've implemented three noise-identification algorithms based on Stable32-documentation and other papers: B1, R(n), and Lag-1 autocorrelation.

B1 (Howe 2000, Barnes1969) is defined as the ratio of the standard N-sample variance to the (2-sample) Allan variance. From the definitions one can derive an expected B1 ratio of (the length of the time-series is N)

where mu is the tau-exponent of Allan variance for the noise-slope  defined by b (or a). Since mu is the same (-2) for both b=0 and b=-1  (red and green data) we can't use B1 to resolve between these noise-types. B1 looks like a good noise-identifier for b=[-2, -3, -4] where it resolves very well between the noise types at short tau, and slightly worse at longer tau.

R(n) can be used to resolve between b=0 and b=-1. It is defined as the ratio MVAR/AVAR, and resolves between noise types because MVAR and AVAR have different tau-slopes mu. For b=0 we expect mu(AVAR, b=0) = -2 while mu(MVAR, b=0)=-3 so we get mu(R(n), b=0)=-1 (red data points/line). For b=-1 (green) the usual tables predict the same mu for MVAR and AVAR, but there's a weak log(tau) dependence in the prefactor (see e.g. Dawkins2007, or IEEE1139). For the other noise-types b=[-2,-3,-4] we can't use R(n) because the predicted ratio is one for all these noise types. In contrast to B1 the noise identification using R(n) works best at large tau (and not at all at tau=tau0 or AF=1).

The lag-1 autocorrelation method (Riley, Riley & Greenhall 2004) is the newest, and uses the predicted lag-1 autocorrelation for (WPM b=0, FPM b=-1, WFM b=-2) to identify noise. For other noise types we differentiate the time-series, which adds +2 to the noise slope, until we recognize the noise type.

Here are three figures for ACF, B1, and R(n) noise identification where a simulated time series with known power law noise is first generated using the Kasdin&Walter algorithm, and then we try to identify the noise slope.

For Lag-1 ACF when we decimate the phase time-series for AF>1 there seems to be a bias to the predicted a (alpha) for b=-1, b=-3, b=-4 which I haven't seen described in the papers or understand that well. Perhaps an aliasing effect(??).

 

AllanTools 2016.11 - now with Confidence Intervals!

at2016-11_wtih_ci

I've added confidence interval estimation to allantools, based on a 2004 paper by Greenhall & Riley: "Uncertainty of stability variances based on finite differences"

So far not much is automated so you have to run everything manually. After a normal call to allantools.adev() to calculate the ADEV we loop through each (tau, adev) pair and first call allantools.edf_greenhall() to get the number of equivalent-degrees-of-freedom (EDF), and then evaluate a confidence interval with allantools.confidence_interval(). A knowledge or estimate of the noise type "alpha" is required for edf_greenhall() - here we just assume alpha=0.

This example is on github at: https://github.com/aewallin/allantools/blob/master/examples/ci_demo.py

import numpy
import matplotlib.pyplot as plt
 
import allantools as at
 
# this demonstrates how to calculate confidence intervals for ADEV
# using the algorithms from Greenhall2004
data_file = '../tests/phasedat/PHASE.DAT'
 
def read_datafile(filename):
    p = []
    with open(filename) as f:
        for line in f:
            if not line.startswith("#"):  # skip comments
                p.append(float(line))
    return p
 
# read input data from file
phase = read_datafile(data_file)
# normal ADEV computation, giving naive 1/sqrt(N) errors
(taus,devs,errs,ns) = at.adev(phase, taus='octave')
 
# Confidence-intervals for each (tau,adev) pair separately.
cis=[]
for (t,dev) in zip(taus,devs):
    # Greenhalls EDF (Equivalent Degrees of Freedom)
    # alpha     +2,...,-4   noise type, either estimated or known
    # d         1 first-difference variance, 2 allan variance, 3 hadamard variance
    #           we require: alpha+2*d >1     (is this ever false?)
    # m         tau/tau0 averaging factor
    # N         number of phase observations
    edf = at.edf_greenhall( alpha=0, d=2, m=t, N=len(phase), overlapping = False, modified=False )
    # with the known EDF we get CIs 
    # for 1-sigma confidence we set
    # ci = scipy.special.erf(1/math.sqrt(2)) = 0.68268949213708585
    (lo,hi) = at.confidence_intervals( dev=dev, ci=0.68268949213708585, edf=edf )
    cis.append( (lo,hi) )
 
# now we are ready to print and plot the results
print "Tau\tmin Dev\t\tDev\t\tMax Dev"
for (tau,dev,ci) in zip(taus,devs,cis):
    print "%d\t%f\t%f\t%f" % (tau, ci[0], dev, ci[1] )
""" output is
Tau	min Dev		Dev		Max Dev
1	0.285114	0.292232	0.299910
2	0.197831	0.205102	0.213237
4	0.141970	0.149427	0.158198
8	0.102541	0.110135	0.119711
16	0.056510	0.062381	0.070569
32	0.049153	0.056233	0.067632
64	0.027109	0.032550	0.043536
128	0.026481	0.033855	0.055737
256	0.007838	0.010799	0.031075
"""
plt.figure(figsize=(12,8))
plt.gca().set_yscale('log')
plt.gca().set_xscale('log')
err_lo = [ d-ci[0] for (d,ci) in zip(devs,cis)]
err_hi = [ ci[1]-d for (d,ci) in zip(devs,cis)]
 
plt.errorbar(taus, devs, yerr=[ err_lo, err_hi ] ,fmt='o')
plt.grid()
plt.xlabel('Tau (s)')
plt.ylabel('ADEV')
plt.title('AllanTools 2016.11 - now with Confidence Intervals!')
# just to check plot the intervals as dots also
plt.plot(taus, [ci[0] for ci in cis],'r.')
plt.plot(taus, [ci[1] for ci in cis],'g.')
 
plt.show()

scipy.stats.chi2.ppf() without scipy

Allantools has a dependence on scipy because it uses scipy.stats.chi2.ppf() (inverse of the chi-squared cumulative distribution function) in the code for confidence intervals.

When testing scipy takes quite a long time to install and the whole package seems a bit overkill for just this one function.

So I tried implementing it using just numpy. It sort of works, but not for corner cases where p is very close to 1.0 or k is a big number. I get for example:

    top = pow(x, s)*math.exp(-x)*pow(x,k)
OverflowError: (34, 'Numerical result out of range')

Maybe there's something trick when numerically evaluating lower_gamma() using the series expansion that I am missing...

import scipy.stats
import math
import numpy
 
def bisection(function, k, p, a, b, tol):
	# http://code.activestate.com/recipes/578417-bisection-method-in-python/
	assert (function(a,k)-p)*(function(b,k)-p) < 0 # a, b must bracket root
	c = (a+b)/2.0
	while (b-a)/2.0 > tol:
		if (function(c, k)-p) == 0:
			return c
		elif (function(a,k)-p)*(function(c,k)-p) < 0:
			b = c
		else :
			a = c
		c = (a+b)/2.0
	return c
 
def lower_gamma(s,x):
	# lower incomplete gamma function
	# https://en.wikipedia.org/wiki/Incomplete_gamma_function#Evaluation_formulae
	g  = 0
	last_g = 1.0
	done = False
	tol = 1.0e-6
	k=0
	while not done:
		top = pow(x, s)*math.exp(-x)*pow(x,k)
		bot = numpy.prod( [float(s+j) for j in range(k+1) ] )
		dg = float(top)/float(bot)
		if dg == float("Inf"):
			break
		g += dg
		k += 1
		if k>100: # get at least 100 terms in the sum
			if g==0:
				break
			delta = abs(dg/g)
			if delta == float("Inf"):
				break
			if delta < tol:
				done = True
		last_g = g
	return g
 
def chi2_cdf(x, k):
	# chi-squared cumulative density function
	# cdf(x; k) = lower_gamma(k/2, x/2) / gamma(k/2)
	return lower_gamma(k/2.0, x/2.0) / math.gamma(k/2.0)
 
def chi2_ppf(p, k):
	# chi-squared Percent point function (inverse of cdf percentiles).
	# look for x such that
	# p = chi2_cdf( x=chi2_ppf(p, k), k)
	tol = 1e-8
	lolim = 0
	hilim = k
	while (chi2_cdf(lolim,k)-p)*(chi2_cdf(hilim,k)-p) > 0: 
		hilim *= 1.5
	return bisection( chi2_cdf, k, p, lolim, hilim, tol)
 
print "scipy cdf: ",scipy.stats.chi2.cdf(55, 33)	
print "own   cdf: ",chi2_cdf(55, 33)
 
 
print "scipy ppf ", scipy.stats.chi2.ppf(0.4, 33)
print "  own ppf ", chi2_ppf(0.4, 33)
 
# test that we really found the inverse
print scipy.stats.chi2.cdf(scipy.stats.chi2.ppf(0.4, 33), 33)
print chi2_cdf( chi2_ppf(0.4, 33), 33 )
 
# try to check the scipy function against our own function
# for some random input of (p, k)
for n in range(100):
	k = numpy.random.randint(20, 200)
	p = numpy.random.random()
	print k, p,
	a=scipy.stats.chi2.ppf(p, k)
	b=chi2_ppf(p, k)
	ok = numpy.isclose(a, b)
	if ok:
		print  ok
	else:
		print  ok, a, b
	assert ok

Project badges

New shiny project badges for allantools!
badges

Five colours of noise

Update: now with the colours matching in all graphs:

colorednoise

Time-series generated with colorednoise (following Kasdin&Walter), power-spectral-densities and Allan deviations computed with allantools, and compared to theoretical predictions in IEEE1139-2008.

colorednoise

The PSD lines and MDEV lines seem spot-on, but are the ADEV lines systematically a bit low?

Code here: example_noise_slopes.py

AllanTools 2016.3 benchmark

Update: a figure with more data points:

allantools.2016.3.benchmark.1e8

I've released AllanTools 2016.3 which now contains new mtotdev(), htotdev(), and theo1() statistics along with many other improvements. Here's a benchmark:

allantools2016.3.benchmark

Compare to this one (from here):

stable32.benchmarkSee also: numpy vs pure python comparison from 2014 August.

 

Hadamard total deviation in allantools

Following on from modified total deviation mtotdev() the Hadamard total deviation htotdev() algorithm is very similar but instead of phase data takes frequency data. Now included in allantools.

Here's a comarison against Stable32 and the NIST SP 1065 table values.

There's no bias-correction for now, and apparently it is customary not to use htotdev(m=1) at an averaging-factor of 1, but instead use ohdev(m=1). This is why the 'raw' value from allantools at tau=1 in the plot below is a factor of 2 too low.

htotdev_2016-03-27Both mtotdev() and htotdev() are very slow algorithms - help with making them faster would be appreciated!

Modified Total Deviation in allantools

I wrote a first rough (and very slow!) implementation of Modified Total Deviation mtotdev() for allantools.

mtotdev() combines the features of modified Allan deviation mdev() (being able to distinguish between white and flicker phase modulation) and Total deviation totdev() (better confidence intervals at large tau).

Here are some results. The Time Total Deviation ttotdev() follows trivially from this work also, since it is only a scaled version of mtotdev(). I used the "NBS14" 1000-point frequency dataset and compared my results against Stable32 and those in NIST SP 1065 (Table 31, page 108).

mtotdev_comparison_AW2016-03-24

ttotdev_comparison_AW2016-03-24

The figures show mtotdev() and ttotdev() from Stable32 runs and allantools. I've also added mdev() and tdev() traces to compare against. At first sight this looks strange, but mtotdev() is a biased estimator, and Stable32 applies a bias correction which explains the results.

Somewhat surprisingly Stable32 applies a bias-correction only when run in the "all-tau" mode. These numbers agree with those from the NIST SP 1065 table. For this dataset Stable32 is undecided on what power-law the dataset follows at large tau, which results in deviations that jump up and down (because a different bias-correction is applied at different tau, red datapoints).

When Stable32 is run in "octave-tau" or "decade-tau" mode no bias correction is applied. These numbers agree with the ones from allantools.mtotdev().

mtotdev_bias_AW2016-03-24

This figure shows the ratio of variances between allantools.mtotdev() (no bias correction) and a Stable32 all-tau run (bias correction applied). The lines correspond to the bias-correction values for different noise processes.

There also seems to be a misprint in NIST SP 1065 equation (28) page 26, where it says ttotdev() is scaled by tau-cubed (when tau-squared is correct). Who reads these things anyway - not many it seems 😉

Phase noise with AllanTools

I've looked at calculating phase-noise spectra with python - to be included in allantools. Here are some first results.

white_pm_phasenoise

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