Source code for gammapy.stats.feldman_cousins

# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Feldman Cousins algorithm to compute parameter confidence limits."""
import logging
import numpy as np
import scipy.stats

__all__ = [
    "fc_find_acceptance_interval_gauss",
    "fc_find_acceptance_interval_poisson",
    "fc_construct_acceptance_intervals_pdfs",
    "fc_get_limits",
    "fc_fix_limits",
    "fc_find_limit",
    "fc_find_average_upper_limit",
    "fc_construct_acceptance_intervals",
]

log = logging.getLogger(__name__)


[docs]def fc_find_acceptance_interval_gauss(mu, sigma, x_bins, alpha): r""" Analytical acceptance interval for Gaussian with boundary at the origin. .. math:: \int_{x_{min}}^{x_{max}} P(x|mu)\mathrm{d}x = alpha For more information see :ref:`documentation <feldman_cousins>`. Parameters ---------- mu : float Mean of the Gaussian sigma : float Width of the Gaussian x_bins : array-like Bins in x alpha : float Desired confidence level Returns ------- (x_min, x_max) : tuple of floats Acceptance interval """ dist = scipy.stats.norm(loc=mu, scale=sigma) x_bin_width = x_bins[1] - x_bins[0] p = [] r = [] for x in x_bins: p.append(dist.pdf(x) * x_bin_width) # This is the formula from the FC paper if mu == 0 and sigma == 1: if x < 0: r.append(np.exp(mu * (x - mu * 0.5))) else: r.append(np.exp(-0.5 * np.power((x - mu), 2))) # This is the more general formula else: # Implementing the boundary condition at zero mu_best = max(0, x) prob_mu_best = scipy.stats.norm.pdf(x, loc=mu_best, scale=sigma) # probMuBest should never be zero. Check it just in case. if prob_mu_best == 0.0: r.append(0.0) else: r.append(p[-1] / prob_mu_best) p = np.asarray(p) r = np.asarray(r) if sum(p) < alpha: raise ValueError( "X bins don't contain enough probability to reach " "desired confidence level for this mu!" ) rank = scipy.stats.rankdata(-r, method="dense") index_array = np.arange(x_bins.size) rank_sorted, index_array_sorted = zip(*sorted(zip(rank, index_array))) index_min = index_array_sorted[0] index_max = index_array_sorted[0] p_sum = 0 for i in range(len(rank_sorted)): if index_array_sorted[i] < index_min: index_min = index_array_sorted[i] if index_array_sorted[i] > index_max: index_max = index_array_sorted[i] p_sum += p[index_array_sorted[i]] if p_sum >= alpha: break return x_bins[index_min], x_bins[index_max] + x_bin_width
[docs]def fc_find_acceptance_interval_poisson(mu, background, x_bins, alpha): r"""Analytical acceptance interval for Poisson process with background. .. math:: \int_{x_{min}}^{x_{max}} P(x|mu)\mathrm{d}x = alpha For more information see :ref:`documentation <feldman_cousins>`. Parameters ---------- mu : float Mean of the signal background : float Mean of the background x_bins : array-like Bins in x alpha : float Desired confidence level Returns ------- (x_min, x_max) : tuple of floats Acceptance interval """ dist = scipy.stats.poisson(mu=mu + background) x_bin_width = x_bins[1] - x_bins[0] p = [] r = [] for x in x_bins: p.append(dist.pmf(x)) # Implementing the boundary condition at zero muBest = max(0, x - background) probMuBest = scipy.stats.poisson.pmf(x, mu=muBest + background) # probMuBest should never be zero. Check it just in case. if probMuBest == 0.0: r.append(0.0) else: r.append(p[-1] / probMuBest) p = np.asarray(p) r = np.asarray(r) if sum(p) < alpha: raise ValueError( "X bins don't contain enough probability to reach " "desired confidence level for this mu!" ) rank = scipy.stats.rankdata(-r, method="dense") index_array = np.arange(x_bins.size) rank_sorted, index_array_sorted = zip(*sorted(zip(rank, index_array))) index_min = index_array_sorted[0] index_max = index_array_sorted[0] p_sum = 0 for i in range(len(rank_sorted)): if index_array_sorted[i] < index_min: index_min = index_array_sorted[i] if index_array_sorted[i] > index_max: index_max = index_array_sorted[i] p_sum += p[index_array_sorted[i]] if p_sum >= alpha: break return x_bins[index_min], x_bins[index_max] + x_bin_width
[docs]def fc_construct_acceptance_intervals_pdfs(matrix, alpha): r"""Numerically choose bins a la Feldman Cousins ordering principle. For more information see :ref:`documentation <feldman_cousins>`. Parameters ---------- matrix : array-like A list of x PDFs for increasing values of mue. alpha : float Desired confidence level Returns ------- distributions_scaled : ndarray Acceptance intervals (1 means inside, 0 means outside) """ number_mus = len(matrix) distributions_scaled = np.asarray(matrix) distributions_re_scaled = np.asarray(matrix) summed_propability = np.zeros(number_mus) # Step 1: # For each x, find the greatest likelihood in the mu direction. # greatest_likelihood is an array of length number_x_bins. greatest_likelihood = np.amax(distributions_scaled, axis=0) # Set to some value if none of the bins has an entry to avoid # division by zero greatest_likelihood[greatest_likelihood == 0] = 1 # Step 2: # Scale all entries by this value distributions_re_scaled /= greatest_likelihood # Step 3 (Feldman Cousins Ordering principle): # For each mu, get the largest entry largest_entry = np.argmax(distributions_re_scaled, axis=1) # Set the rank to 1 and add probability for i in range(number_mus): distributions_re_scaled[i][largest_entry[i]] = 1 summed_propability[i] += np.sum( np.where(distributions_re_scaled[i] == 1, distributions_scaled[i], 0) ) distributions_scaled[i] = np.where( distributions_re_scaled[i] == 1, 1, distributions_scaled[i] ) # Identify next largest entry not yet ranked. While there are entries # smaller than 1, some bins don't have a rank yet. while np.amin(distributions_re_scaled) < 1: # For each mu, this is the largest rank attributed so far. largest_rank = np.amax(distributions_re_scaled, axis=1) # For each mu, this is the largest entry that is not yet a rank. largest_entry = np.where( distributions_re_scaled < 1, distributions_re_scaled, -1 ) # For each mu, this is the position of the largest entry that is not yet a rank. largest_entry_position = np.argmax(largest_entry, axis=1) # Invalidate indices where there is no maximum (every entry is already a rank) largest_entry_position = [ largest_entry_position[i] if largest_entry[i][largest_entry_position[i]] != -1 else -1 for i in range(len(largest_entry_position)) ] # Replace the largest entry with the highest rank so far plus one # Add the probability for i in range(number_mus): if largest_entry_position[i] == -1: continue distributions_re_scaled[i][largest_entry_position[i]] = largest_rank[i] + 1 if summed_propability[i] < alpha: summed_propability[i] += distributions_scaled[i][ largest_entry_position[i] ] distributions_scaled[i][largest_entry_position[i]] = 1 else: distributions_scaled[i][largest_entry_position[i]] = 0 return distributions_scaled
[docs]def fc_get_limits(mu_bins, x_bins, acceptance_intervals): r"""Find lower and upper limit from acceptance intervals. For more information see :ref:`documentation <feldman_cousins>`. Parameters ---------- mu_bins : array-like The bins used in mue direction. x_bins : array-like The bins of the x distribution acceptance_intervals : array-like The output of fc_construct_acceptance_intervals_pdfs. Returns ------- lower_limit : array-like Feldman Cousins lower limit x-coordinates upper_limit : array-like Feldman Cousins upper limit x-coordinates x_values : array-like All the points that are inside the acceptance intervals """ upper_limit = [] lower_limit = [] x_values = [] number_mu = len(mu_bins) number_bins_x = len(x_bins) for mu in range(number_mu): upper_limit.append(-1) lower_limit.append(-1) x_values.append([]) acceptance_interval = acceptance_intervals[mu] for x in range(number_bins_x): # This point lies in the acceptance interval if acceptance_interval[x] == 1: x_value = x_bins[x] x_values[-1].append(x_value) # Upper limit is first point where this condition is true if upper_limit[-1] == -1: upper_limit[-1] = x_value # Lower limit is first point after this condition is not true if x == number_bins_x - 1: lower_limit[-1] = x_value else: lower_limit[-1] = x_bins[x + 1] return lower_limit, upper_limit, x_values
[docs]def fc_fix_limits(lower_limit, upper_limit): r"""Push limits outwards as described in the FC paper. For more information see :ref:`documentation <feldman_cousins>`. Parameters ---------- lower_limit : array-like Feldman Cousins lower limit x-coordinates upper_limit : array-like Feldman Cousins upper limit x-coordinates """ all_fixed = False while not all_fixed: all_fixed = True for j in range(1, len(upper_limit)): if upper_limit[j] < upper_limit[j - 1]: upper_limit[j - 1] = upper_limit[j] all_fixed = False for j in range(1, len(lower_limit)): if lower_limit[j] < lower_limit[j - 1]: lower_limit[j] = lower_limit[j - 1] all_fixed = False
[docs]def fc_find_limit(x_value, x_values, y_values): r"""Find the limit for a given x measurement. See also: :ref:`feldman_cousins` Parameters ---------- x_value : float The measured x value for which the upper limit is wanted. x_values : array-like The x coordinates of the confidence belt. y_values : array-like The y coordinates of the confidence belt. Returns ------- limit : float The Feldman Cousins limit """ if x_value > max(x_values): raise ValueError("Measured x outside of confidence belt!") # Loop through the x-values in reverse order for i in reversed(range(len(x_values))): current_x = x_values[i] # The measured value sits on a bin edge. In this case we want the upper # most point to be conservative, so it's the first point where this # condition is true. if x_value == current_x: return y_values[i] # If the current value lies between two bins, take the higher y-value # in order to be conservative. if x_value > current_x: return y_values[i + 1]
[docs]def fc_find_average_upper_limit(x_bins, matrix, upper_limit, mu_bins, prob_limit=1e-5): r"""Calculate the average upper limit for a confidence belt. See also: :ref:`feldman_cousins` Parameters ---------- x_bins : array-like Bins in x direction matrix : array-like A list of x PDFs for increasing values of mue (same as for fc_construct_acceptance_intervals_pdfs). upper_limit : array-like Feldman Cousins upper limit x-coordinates mu_bins : array-like The bins used in mue direction. prob_limit : float Probability value at which x values are no longer considered for the average limit. Returns ------- average_limit : float Average upper limit """ average_limit = 0 number_points = len(x_bins) for i in range(number_points): # Bins with very low probability will not contribute to average limit if matrix[0][i] < prob_limit: continue try: limit = fc_find_limit(x_bins[i], upper_limit, mu_bins) except: log.warning("Warning: Calculation of average limit incomplete!") log.warning("Add more bins in mu direction or decrease prob_limit.") return average_limit average_limit += matrix[0][i] * limit return average_limit
[docs]def fc_construct_acceptance_intervals(distribution_dict, bins, alpha): r"""Convenience function that calculates the PDF for the user. For more information see :ref:`documentation <feldman_cousins>`. Parameters ---------- distribution_dict : dict Keys are mu values and value is an array-like list of x values bins : array-like The bins the x distribution will have alpha : float Desired confidence level Returns ------- acceptance_intervals : ndarray Acceptance intervals (1 means inside, 0 means outside) """ distributions_scaled = [] # Histogram gets rid of the last bin, so add one extra bin_width = bins[1] - bins[0] new_bins = np.concatenate((bins, np.array([bins[-1] + bin_width])), axis=0) # Histogram and normalise each distribution so it is a real PDF for _, distribution in sorted(distribution_dict.items()): entries = np.histogram(distribution, bins=new_bins)[0] integral = float(sum(entries)) distributions_scaled.append(entries / integral) acceptance_intervals = fc_construct_acceptance_intervals_pdfs( distributions_scaled, alpha ) return acceptance_intervals