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SuzUtils - Suzanne Aigrain This repository contains miscellaneous bits of code I have written or pilfered, which I use often, and which I thought might be useful to others, but weren't substantial enough to warrant their own repository. I have tried to document each routine / module reasonably well. Comments / feedback welcome! Also please let me know if you make significant improvements to any of these that you think I should incorporate. Currently included (last updated December 2013) - periodograms: Various tools for time-series analysis in the Fourier domain. - sinefit: least squares fitting of sine curves to a time-series with arbitrary time-sampling (this is a generalisation of the Lomb-Scargle periodogram, but it doesn't include the false alarm probability and significance measures, which are almost always misleading anyway) - DftPowerspectrum: compute and plot the power spectrum of a regularly sampled time-series using the discrete FFT (shows how to get the normalisation right, and which frequencies correspond to which element in the array) - AcfPeriodogram: compute and plot the ACF of a regularly sampled time-series and its amplitude spectrum (also known as the periodogram of the time-series), after optional smoothing. - filter: routines to filter time-series (or any 1-D dataset) - filt1d: combination of linear (boxcar or gauss) and median filter, with edge reflection or circular edge criterion - boxcare: boxcar (moving average) filter with edge reflection or circular edge criterion - gausse: Gaussian (tapered window) filter with edge reflection or circular edge criterion - NIF: iterative version of filt1d with k-sigma clipping (Aigrain & Irwin 2004) - norm: NaN-robust wrappers for min, max, mean, median, sum, plus routines to compute median and MAD-estimated scatter, to normalise to zero mean and unit variance, and to scale to range from 0 to 1. - multiplot: routines to make plots with shared axes - mpfit: non-linear least squares optimization using Levenberg-Marquart algorithm, with option to fix or bound some parameters. Adapted by me from a really old version that was itself adapted from the IDL routine of the same name. Horribly cumbersome and rather unstable but quite useful because very generic. - show_cmaps.py: little script to display the available color maps - extrema.py: returns indices and values of the extrema of an array - GP_simple: ultra-simple GP regression code, useful to show complete GP newbies just how simple it all is - GP_suz: a slightly more sophisticated GP regression code designed to be called from other programs. Includes a range of kernel functions, and a transit mean function (using Tom Evans's planetc module) - ask me if you want some other kernel or mean functions added. Also includes functions to tune the parameters using max-likelihood (scipy.optmize.fmin) or a simple Metropolis-Hastings MCMC. The likelihood can be combined with priors to explore a posterior distribution but at the moment only Gaussian priors are implemented. - spot_model: generate light and radial velocity curves for active stars using a very simple spot model (no faculae, no penumbra). There are two options, one that includes limb-darkening and projection effects over the spots, using the formalism of Dorren (1989) for circular spots, but is slow, and one that ignores these effects, but is very fast. The user can set the stellar radius and inclination, the (linear) limb-darkening coefficient for the photosphere, the number of spots, and the effective size (size * contrast), longitude, latitude, limb-darkening coefficient, and rotation period of each spot. Spot evolution can also be included, in this case the effective size of each spot varies according to a bell-shaped (Gaussian) curve with standard deviation and peak time specified by the user. The code incluces user-friendly routines for generating and plotting either regularly sampled time-series, or irregularly-sampled time-series more typical of ground-based observations, as well as their periodograms. - orbit: compute sky coordinates and radial velocities for star or planet in two-body Keplerian system.
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