Astrostatistics Tools (astropy.stats)

Introduction

The astropy.stats package holds statistical functions or algorithms used in astronomy. While the scipy.stats and statsmodels packages contains a wide range of statistical tools, they are general-purpose packages and are missing some tools that are particularly useful or specific to astronomy. This package is intended to provide such functionality, but not to replace scipy.stats if its implementation satisfies astronomers’ needs.

Getting Started

A number of different tools are contained in the stats package, and they can be accessed by importing them:

>>> from astropy import stats

A full list of the different tools are provided below. Please see the documentation for their different usages. For example, sigma clipping, which is a common way to estimate the background of an image, can be performed with the sigma_clip() function. By default, the function returns a masked array where outliers are masked.

Examples

To estimate the background of an image:

>>> data = [1, 5, 6, 8, 100, 5, 3, 2]
>>> stats.sigma_clip(data, sigma=2, maxiters=5)
masked_array(data=[1, 5, 6, 8, --, 5, 3, 2],
             mask=[False, False, False, False,  True, False, False, False],
       fill_value=999999)

Alternatively, the SigmaClip class provides an object-oriented interface to sigma clipping, which also returns a masked array by default:

>>> sigclip = stats.SigmaClip(sigma=2, maxiters=5)
>>> sigclip(data)
masked_array(data=[1, 5, 6, 8, --, 5, 3, 2],
             mask=[False, False, False, False,  True, False, False, False],
       fill_value=999999)

In addition, there are also several convenience functions for making the calculation of statistics even more convenient. For example, sigma_clipped_stats() will return the mean, median, and standard deviation of a sigma-clipped array:

>>> stats.sigma_clipped_stats(data, sigma=2, maxiters=5)  
(4.2857142857142856, 5.0, 2.2497165354319457)

There are also tools for calculating robust statistics, sampling the data, circular statistics, confidence limits, spatial statistics, and adaptive histograms.

Most tools are fairly self-contained, and include relevant examples in their docstrings.

Constants

The astropy.stats package defines two constants useful for converting between Gaussian sigma and full width at half maximum (FWHM):

gaussian_sigma_to_fwhm

Factor with which to multiply Gaussian 1-sigma standard deviation to convert it to full width at half maximum (FWHM).

>>> from astropy.stats import gaussian_sigma_to_fwhm
>>> gaussian_sigma_to_fwhm  
2.3548200450309493
gaussian_fwhm_to_sigma

Factor with which to multiply Gaussian full width at half maximum (FWHM) to convert it to 1-sigma standard deviation.

>>> from astropy.stats import gaussian_fwhm_to_sigma
>>> gaussian_fwhm_to_sigma  
0.42466090014400953

See Also

  • scipy.stats

    This SciPy package contains a variety of useful statistical functions and classes. The functionality in astropy.stats is intended to supplement this, not replace it.

  • statsmodels

    The statsmodels package provides functionality for estimating different statistical models, tests, and data exploration.

  • astroML

    The astroML package is a Python module for machine learning and data mining. Some of the tools from this package have been migrated here, but there are still a number of tools there that are useful for astronomy and statistical analysis.

  • astropy.visualization.hist()

    The histogram() routine and related functionality defined here are used within the astropy.visualization.hist() function. For a discussion of these methods for determining histogram binnings, see Choosing Histogram Bins.

Performance Tips

If you are finding sigma clipping to be slow, and if you have not already done so, consider installing the bottleneck package, which will speed up some of the internal computations. In addition, if you are using standard functions for cenfunc and/or stdfunc, make sure you specify these as strings rather than passing a NumPy function — that is, use:

>>> sigma_clip(array, cenfunc='median')  

instead of:

>>> sigma_clip(array, cenfunc=np.nanmedian)  

Using strings will allow the sigma-clipping algorithm to pick the fastest implementation available for finding the median.

Reference/API

astropy.stats Package

This subpackage contains statistical tools provided for or used by Astropy.

While the scipy.stats package contains a wide range of statistical tools, it is a general-purpose package, and is missing some that are particularly useful to astronomy or are used in an atypical way in astronomy. This package is intended to provide such functionality, but not to replace scipy.stats if its implementation satisfies astronomers’ needs.

Functions

binom_conf_interval(k, n[, …])

Binomial proportion confidence interval given k successes, n trials.

binned_binom_proportion(x, success[, bins, …])

Binomial proportion and confidence interval in bins of a continuous variable x.

poisson_conf_interval(n[, interval, sigma, …])

Poisson parameter confidence interval given observed counts

median_absolute_deviation(data[, axis, …])

Calculate the median absolute deviation (MAD).

mad_std(data[, axis, func, ignore_nan])

Calculate a robust standard deviation using the median absolute deviation (MAD).

signal_to_noise_oir_ccd(t, source_eps, …)

Computes the signal to noise ratio for source being observed in the optical/IR using a CCD.

bootstrap(data[, bootnum, samples, bootfunc])

Performs bootstrap resampling on numpy arrays.

kuiper(data[, cdf, args])

Compute the Kuiper statistic.

kuiper_two(data1, data2)

Compute the Kuiper statistic to compare two samples.

kuiper_false_positive_probability(D, N)

Compute the false positive probability for the Kuiper statistic.

cdf_from_intervals(breaks, totals)

Construct a callable piecewise-linear CDF from a pair of arrays.

interval_overlap_length(i1, i2)

Compute the length of overlap of two intervals.

histogram_intervals(n, breaks, totals)

Histogram of a piecewise-constant weight function.

fold_intervals(intervals)

Fold the weighted intervals to the interval (0,1).

biweight_location(data[, c, M, axis, ignore_nan])

Compute the biweight location.

biweight_scale(data[, c, M, axis, …])

Compute the biweight scale.

biweight_midvariance(data[, c, M, axis, …])

Compute the biweight midvariance.

biweight_midcovariance(data[, c, M, …])

Compute the biweight midcovariance between pairs of multiple variables.

biweight_midcorrelation(x, y[, c, M, …])

Compute the biweight midcorrelation between two variables.

sigma_clip(data[, sigma, sigma_lower, …])

Perform sigma-clipping on the provided data.

sigma_clipped_stats(data[, mask, …])

Calculate sigma-clipped statistics on the provided data.

jackknife_resampling(data)

Performs jackknife resampling on numpy arrays.

jackknife_stats(data, statistic[, …])

Performs jackknife estimation on the basis of jackknife resamples.

circmean(data[, axis, weights])

Computes the circular mean angle of an array of circular data.

circvar(data[, axis, weights])

Computes the circular variance of an array of circular data.

circmoment(data[, p, centered, axis, weights])

Computes the p-th trigonometric circular moment for an array of circular data.

circcorrcoef(alpha, beta[, axis, …])

Computes the circular correlation coefficient between two array of circular data.

rayleightest(data[, axis, weights])

Performs the Rayleigh test of uniformity.

vtest(data[, mu, axis, weights])

Performs the Rayleigh test of uniformity where the alternative hypothesis H1 is assumed to have a known mean angle mu.

vonmisesmle(data[, axis])

Computes the Maximum Likelihood Estimator (MLE) for the parameters of the von Mises distribution.

bayesian_blocks(t[, x, sigma, fitness])

Compute optimal segmentation of data with Scargle’s Bayesian Blocks

histogram(a[, bins, range, weights])

Enhanced histogram function, providing adaptive binnings

scott_bin_width(data[, return_bins])

Return the optimal histogram bin width using Scott’s rule

freedman_bin_width(data[, return_bins])

Return the optimal histogram bin width using the Freedman-Diaconis rule

knuth_bin_width(data[, return_bins, quiet])

Return the optimal histogram bin width using Knuth’s rule.

calculate_bin_edges(a[, bins, range, weights])

Calculate histogram bin edges like numpy.histogram_bin_edges.

bayesian_info_criterion(log_likelihood, …)

Computes the Bayesian Information Criterion (BIC) given the log of the likelihood function evaluated at the estimated (or analytically derived) parameters, the number of parameters, and the number of samples.

bayesian_info_criterion_lsq(ssr, n_params, …)

Computes the Bayesian Information Criterion (BIC) assuming that the observations come from a Gaussian distribution.

akaike_info_criterion(log_likelihood, …)

Computes the Akaike Information Criterion (AIC).

akaike_info_criterion_lsq(ssr, n_params, …)

Computes the Akaike Information Criterion assuming that the observations are Gaussian distributed.

Classes

SigmaClip([sigma, sigma_lower, sigma_upper, …])

Class to perform sigma clipping.

FitnessFunc([p0, gamma, ncp_prior])

Base class for bayesian blocks fitness functions

Events([p0, gamma, ncp_prior])

Bayesian blocks fitness for binned or unbinned events

RegularEvents(dt[, p0, gamma, ncp_prior])

Bayesian blocks fitness for regular events

PointMeasures([p0, gamma, ncp_prior])

Bayesian blocks fitness for point measures

RipleysKEstimator(area[, x_max, y_max, …])

Estimators for Ripley’s K function for two-dimensional spatial data.

Class Inheritance Diagram

Inheritance diagram of astropy.stats.sigma_clipping.SigmaClip, astropy.stats.bayesian_blocks.FitnessFunc, astropy.stats.bayesian_blocks.Events, astropy.stats.bayesian_blocks.RegularEvents, astropy.stats.bayesian_blocks.PointMeasures, astropy.stats.spatial.RipleysKEstimator