Lomb-Scargle Periodogram

One of the best known methods for detecting periodicity in unevenly-sampled time series is the Lomb-Scargle Periodogram. gatspy has three main implementations of the classic periodogram:

This basic method uses simple linear algebra to compute the periodogram. Though it is relatively slow, the approach allows for some enhancements such as floating mean, multiple Fourier terms, and regularization terms.
This class implements the fast, O[N logN] implementation of the Lomb-Scargle periodogram. It is much faster than either of the below methods, especially as the number of data points and frequencies increases. It is limited to either a simple pre-centered model or a floating mean model, and the frequencies must be computed on a regular grid.
This class depends on the Lomb-Scargle implementation in astroML. This is a cython implementation, and is slightly faster than LombScargle, though it does not handle higher-order fits or regularization. It is mainly implemented for the sake of unit testing.

For the basic no-frills Lomb-Scargle algorithm, the best option to use is LombScargleFast. Keep in mind that aside from options used at model instantiation, the API of the three is identical.

API of Periodic Models

The periodogram models here follow in the vein of the scikit-learn API, which makes clear the separation between several parts of the problem:

  • the choice of model: this happens at class instantiation.
  • the fitting of the model to data: this happens with the fit() method.
  • the application of the model to new data: this happens with the predict() method.
  • the evaluation of the model fit: this happens with the score() method.

The models in gatspy differ from those in scikit-learn in several important ways:

  1. The fit() method optionally accepts errors in the magnitude inputs. For multiband methods, the fit method also accepts a specification of the filter/band in which the magnitude is observed.
  2. The predict() and score() methods require specification of a period. If this period is not supplied, the best period will be found automatically via an exhaustive grid search, which can be very slow for some models and/or datasets!

We’ll see examples of this below.

Basic Lomb-Scargle Periodogram

We’ll start by looking at the basic Lomb-Scargle Periodogram, using the LombScargleFast model. Let’s start by loading one r-band RR Lyrae lightcurve using the gatspy.datasets.fetch_rrlyrae() function, which is discussed more fully in Datasets (gatspy.datasets).

In [1]: from gatspy import datasets, periodic

In [2]: rrlyrae = datasets.fetch_rrlyrae()

In [3]: lcid = rrlyrae.ids[0]

In [4]: t, mag, dmag, filts = rrlyrae.get_lightcurve(lcid)

In [5]: mask = (filts == 'r')

In [6]: t_r, mag_r, dmag_r = t[mask], mag[mask], dmag[mask]

Given this data, we’d like to determine the best period using the periodogram. This can be done using the find_best_period method of any of the above estimators, once the period_range attribute of the optimizer is set (see discussion below).

Let’s quickly demonstrate this with LombScargleFast. Because our data is from an RR Lyrae star, we’ll set a conservative period range of 0.2 to 1.2 days to make sure it contains the true period:

In [7]: model = periodic.LombScargleFast(fit_period=True)

In [8]: model.optimizer.period_range = (0.2, 1.2)

In [9]: model.fit(t_r, mag_r, dmag_r);

Now the best period is found in the best_period attribute of the model:

In [10]: model.best_period
Out[10]: 0.61431661211675215

The periodogram optimizer uses a two-step grid search, first searching a relatively coarse grid to find several candidate frequencies, and finally zooming-in on these to compute the observed period to high precision. Let’s see how close this period is to the period measured by Sesar 2010 using template fits:

In [11]: metadata = rrlyrae.get_metadata(lcid)

In [12]: true_period = metadata['P']

In [13]: true_period
Out[13]: 0.61431831

The two periods differ to about 10^{-6} days, or approximately one tenth of a second. To see more about what is going on in the periodogram, let’s plot the Lomb-Scargle periodogram as a function of period:

(Source code, png, hires.png, pdf)


We see here why so many steps are needed to find the optimal period: the width of each of these peaks is so small that a coarser grid might easily miss a significant peak!

The Lomb-Scargle model is essentially a least squares fit of a single sinusoid to the data; we can see the model fit using the predict method of the periodic model:

In [14]: import numpy as np

In [15]: tfit = np.linspace(0, model.best_period, 4)

In [16]: model.predict(tfit)
Out[16]: array([ 17.03381525,  17.02560232,  17.37830128,  17.03381525])

Let’s take a look at this model plotted over the phased data:

(Source code, png, hires.png, pdf)


The model is clearly not a good fit for the data (RR Lyrae are much more complicated than a simple sine wave!) but the model serves a useful purpose: it gives us an accurate period determination: the key is that although the sine wave is not a good fit to the data, it is a much better fit at the correct period than it is at the incorrect period.

Configuring the Optimizer

Finding the best period requires use of an optimizer. For typical optimization problems, this is done using some sort of automated minimization scheme such as gradient descent, or perhaps via a Bayesian sampling scheme such as MCMC. Unfortunately, these typical methods fail because there are so many peaks in the periodogram frequency. Typically periodogram studies fall back on a brute force search grid, finding the grid point which maximizes the power/score.

A brute force search has two parameters that must be specified: the range of the grid, and the step spacing of the grid.

The range of the grid must be chosen based on your intuition about the data. Often people wrongly think they can use some sort of Nyquist-type limit to choose a search range (i.e. evaluating based on the minimum or mean time between subsequent observations); unfortunately this line of reasoning does not apply, even approximately, to unequally-spaced observations. This can’t be stressed enough, as such misuse of Nyquist-type arguments comes up often in the literature: The periodogram of an unequally-spaced time series is generally sensitive to periods far smaller than the minimum time between observations. Thus the search range is an entirely free parameter, which must be set by the user based on intuition about the data, and in gatspy is set via the model.optimizer.period_range parameter.

The spacing of the grid is easier to determine automatically. The grid spacing must be much smaller than the width a typical periodogram peak, or you risk entirely missing peaks within the scan. The typical width of a periodogram peak is inversely proportional to the range of the data; that is, if the first observation is at t_{min} and the last observation is at t_{max}, then the peak width in frequency is approximately

\Delta f = 2\pi/(t_{max} - t_{min}).

The grid should be chosen such that multiple grid poins cover each potential peak, so we need to choose an oversampling factor (say, 5) and compute the grid based on this.

We can see all of this in play when we ask the model for the best period. Since we’re looking at RR Lyrae which have typical periods of around 0.5 days, we’ll choose a range around this. Note that the units of period_range should match the units of the times passed to the fit() algorithm. Here the input times are in days, so the period_range is specified as (min_period, max_period) in days:

In [17]: model = periodic.LombScargleFast(fit_period=True)

In [18]: model.optimizer.period_range = (0.2, 1.2)

In [19]: model.fit(t_r, mag_r, dmag_r);

In [20]: model.best_period
Out[20]: 0.61431661211675215

These values can be adjusted via the optimizer argument to the model; this can be done either at or after instantiation. After instantiation is the preferred pattern for the default optimizer:

In [21]: model = periodic.LombScargleFast(fit_period=True)

In [22]: model.optimizer.set(period_range=(0.5, 0.7), first_pass_coverage=10)

In [23]: model.fit(t_r, mag_r, dmag_r);

In [24]: model.best_period
Out[24]: 0.61430890466467969

Before you do any period optimization, be sure to set these quantities appropriately! And note that becuase the grid spacing is equal in frequency, probing small periods (high frequencies) is much more expensive than probing large periods (small frequencies).