Source code for mchammer.data_analysis

import pandas as pd
import numpy as np
import scipy


[docs]def analyze_data(data: np.ndarray, max_lag: int = None) -> dict: """ Carries out an extensive analysis of the data series. Parameters ---------- data data series to compute autocorrelation function for max_lag maximum lag between two data points, used for computing autocorrelation Returns ------- dict calculated properties of the data including, mean, standard deviation, correlation length and a 95% error estimate. """ acf = get_autocorrelation_function(data, max_lag) correlation_length = _estimate_correlation_length_from_acf(acf) error_estimate = _estimate_error(data, correlation_length, confidence=0.95) summary = dict(mean=data.mean(), std=data.std(), correlation_length=correlation_length, error_estimate=error_estimate) return summary
[docs]def get_autocorrelation_function(data: np.ndarray, max_lag: int = None) -> np.ndarray: """ Returns autocorrelation function. The autocorrelation function is computed using `pandas.Series.autocorr <https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.Series.autocorr.html>`_. Parameters ---------- data data series to compute autocorrelation function for max_lag maximum lag between two data points Returns ------- calculated autocorrelation function """ if max_lag is None: max_lag = len(data) - 1 if 1 > max_lag >= len(data): raise ValueError('max_lag should be between 1 and len(data)-1.') series = pd.Series(data) acf = [series.autocorr(lag) for lag in range(0, max_lag)] return np.array(acf)
[docs]def get_correlation_length(data: np.ndarray) -> int: """ Returns estimate of the correlation length of data. The correlation length is taken as the first point where the autocorrelation functions is less than :math:`\\exp(-2)`. If the correlation function never drops below :math:`\\exp(-2)` ``np.nan`` is returned. Parameters ---------- data data series for which to the compute autocorrelation function Returns ------- correlation length """ acf = get_autocorrelation_function(data) correlation_length = _estimate_correlation_length_from_acf(acf) return correlation_length
[docs]def get_error_estimate(data: np.ndarray, confidence: float = 0.95) -> float: """ Returns estimate of standard error :math:`\\mathrm{error}` with confidence interval. .. math:: \\mathrm{error} = t_\\mathrm{factor} * \\mathrm{std}(\\mathrm{data}) / \\sqrt{N_s} where :math:`t_{factor}` is the factor corresponding to the confidence interval and :math:`N_s` is the number of independent measurements (with correlation taken into account). Parameters ---------- data data series for which to estimate the error Returns ------- error estimate """ correlation_length = get_correlation_length(data) error_estimate = _estimate_error(data, correlation_length, confidence) return error_estimate
def _estimate_correlation_length_from_acf(acf: np.ndarray) -> int: """ Estimates correlation length from acf. """ for i, a in enumerate(acf): if a < np.exp(-2): return i return np.nan def _estimate_error(data: np.ndarray, correlation_length: int, confidence: float) -> float: """ Estimates error using correlation length. """ t_factor = scipy.stats.t.ppf((1 + confidence) / 2, len(data)-1) error = t_factor * np.std(data) / np.sqrt(len(data) / correlation_length) return error