Source code for lumin.utils.statistics

import numpy as np
from typing import Tuple, Dict, Optional, Any, Union
import multiprocessing as mp
import math

from statsmodels.nonparametric.kde import KDEUnivariate

__all__ = ['bootstrap_stats', 'get_moments', 'uncert_round']

[docs]def bootstrap_stats(args:Dict[str,Any], out_q:Optional[mp.Queue]=None) -> Union[None,Dict[str,Any]]: r''' Computes statistics and KDEs of data via sampling with replacement Arguments: args: dictionary of arguments. Possible keys are: data - data to resample name - name prepended to returned keys in result dict weights - array of weights matching length of data to use for weighted resampling n - number of times to resample data x - points at which to compute the kde values of resample data kde - whether to compute the kde values at x-points for resampled data mean - whether to compute the means of the resampled data std - whether to compute standard deviation of resampled data c68 - whether to compute the width of the absolute central 68.2 percentile of the resampled data out_q: if using multiporcessing can place result dictionary in provided queue Returns: Result dictionary if `out_q` is `None` else `None`. ''' out_dict, mean, std, c68, boot = {}, [], [], [], [] name = '' if 'name' not in args else args['name'] weights = None if 'weights' not in args else args['weights'] if 'n' not in args: args['n'] = 100 if 'kde' not in args: args['kde'] = False if 'mean' not in args: args['mean'] = False if 'std' not in args: args['std'] = False if 'c68' not in args: args['c68'] = False if args['kde'] and args['data'].dtype != 'float64': data = np.array(args['data'], dtype='float64') else: data = args['data'] len_d = len(data) np.random.seed() for i in range(args['n']): points = np.random.choice(data, len_d, replace=True, p=weights) if args['kde']: kde = KDEUnivariate(points) boot.append([kde.evaluate(x) for x in args['x']]) if args['mean']: mean.append(np.mean(points)) if args['std']: std.append(np.std(points, ddof=1)) if args['c68']: c68.append(np.percentile(np.abs(points), 68.2)) if args['kde']: out_dict[f'{name}_kde'] = boot if args['mean']: out_dict[f'{name}_mean'] = mean if args['std']: out_dict[f'{name}_std'] = std if args['c68']: out_dict[f'{name}_c68'] = c68 if out_q is not None: out_q.put(out_dict) else: return out_dict
[docs]def get_moments(arr:np.ndarray) -> Tuple[float,float,float,float]: r''' Computes mean and std of data, and their associated uncertainties Arguments: arr: univariate data Returns: - mean - statistical uncertainty of mean - standard deviation - statistical uncertainty of standard deviation ''' n = len(arr) m = np.mean(arr) m_4 = np.mean((arr-m)**4) s = np.std(arr, ddof=1) s4 = s**4 se_s2 = ((m_4-(s4*(n-3)/(n-1)))/n)**0.25 se_s = se_s2/(2*s) return m, s/np.sqrt(n), s, se_s
[docs]def uncert_round(value:float, uncert:float) -> Tuple[float,float]: r''' Round value according to given uncertainty using one significant figure of the uncertainty Arguments: value: value to round uncert: uncertainty of value Returns: - rounded value - rounded uncertainty ''' if uncert == math.inf: return value, uncert uncert = np.nan_to_num(uncert) if uncert == 0: return value, uncert factor = 1.0 while uncert / factor > 1: factor *= 10.0 value /= factor uncert /= factor i = 0 while uncert * (10**i) <= 1: i += 1 round_uncert = factor*round(uncert, i) round_value = factor*round(value, i) if int(round_uncert) == round_uncert: round_uncert = int(round_uncert) round_value = int(round_value) return round_value, round_uncert
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