def error_ellipse(x, y, center='mean', level=0.68):
'''compute the position, major axis, minor axis, and position angle
of an ellipse that represents and [level] confidence interval.'''
if center == 'mean':
p1 = mean(x)
p2 = mean(y)
else:
p1 = median(x)
p2 = median(y)
covar = covarc([x, y], center)
eigval, eigvec = linalg.eig(covar)
eigval = map(abs, eigval)
dchi2 = brentq(lambda x: chdtr(2, x) - level, 0, 100)
if eigval[0] > eigval[1]:
major = sqrt(eigval[0] * dchi2)
minor = sqrt(eigval[1] * dchi2)
pa = arctan2(eigvec[1, 0], eigvec[0, 0]) * 180.0 / pi
else:
major = sqrt(eigval[1] * dchi2)
minor = sqrt(eigval[0] * dchi2)
pa = arctan2(eigvec[1, 1], eigvec[0, 1]) * 180.0 / pi
return (p1, p2, major, minor, pa)
def neg_2_log_likelihood_ratio_CDF(l, mu, sigma):
"""Calculate the CDF of -2log(likelihood ratio) CDF.
Parameters
----------
l : float
The :math:`l = \lambda = -2ln(\Lambda)` value to calculate the CDF at.
mu : float
The expectation value to test.
sigma : float
The standard deviation of the distribution.
Returns
-------
prob : float (between 0 and 1)
The probability :math:`CDF(l) = Prob(\lambda < l)`.
"""
# p_lz = stats.norm.cdf(0, loc=mu, scale=sigma)
p_lz = special.ndtr(-mu / sigma)
p_gz = 1 - p_lz
l_crit = mu**2 / sigma**2
# chi2 = stats.chi2(1)
# nu = chi2.cdf(l_crit)
nu = special.chdtr(1, l_crit)
if l < l_crit:
# p_plus = p_gz * 2 * chi2.cdf(l) / (1.0 + nu)
p_plus = p_gz * 2 * special.chdtr(1, l) / (1.0 + nu)
else:
# p_plus = p_gz * (chi2.cdf(l) + nu) / (1.0 + nu)
p_plus = p_gz * (special.chdtr(1, l) + nu) / (1.0 + nu)
tau = 0.5 * sigma**2 / mu * (mu**2 / sigma**2 - l)
if tau < 0:
# p_minus = p_lz - stats.norm.cdf(tau, loc=mu, scale=sigma)
p_minus = p_lz - special.ndtr((tau - mu) / sigma)
else:
p_minus = 0
return p_plus + p_minus
def fit_for_A(self, sep, del_z_bar, N, b_g_rel, c_rel, n, Cov_mat,
covar_type, nbins):
self.c_rel = c_rel
self.get_quad_coeff_for_alpha(b_g_rel, n)
A_step, dA = np.linspace(0., 10., 199, endpoint=True, retstep=True)
prob_step = np.asarray([
np.exp(-0.5 * self.chi_sqrd(A_i, del_z_bar, sep, Cov_mat))
for A_i in A_step
])
prob_step *= 1. / simp_integral(dA, prob_step)
exp_A = simp_integral(dA, prob_step * A_step)
var_A = simp_integral(dA, prob_step * np.power(A_step, 2)) - np.power(
exp_A, 2)
plt.plot(A_step, prob_step)
plt.axvline(x=exp_A, ymin=0, ymax=1, color='k')
plt.axvline(x=exp_A - np.sqrt(var_A),
ymin=0,
ymax=1,
color='k',
linestyle='--')
plt.axvline(x=exp_A + np.sqrt(var_A),
ymin=0,
ymax=1,
color='k',
linestyle='--')
plt.xlabel('A')
plt.ylabel('Probability of fit')
plt.savefig('auto/probability/Prob_A_{0}_{1}.png'.format(
n, covar_type))
plt.close()
CP_A = chdtr(nbins - 1, self.chi_sqrd(0, del_z_bar, sep, Cov_mat))
signif_A = np.sqrt(2) * erfinv(CP_A)
j = (np.where(
np.array([
simp_integral(dA, prob_step[:i])
for i in range(3, A_step.size + 1, 2)
]) > 0.95)[0][0] + 1) * 2
diff = 0.95 - simp_integral(dA, prob_step[:j - 1])
if 0.5 * dA * (prob_step[j - 2] + prob_step[j - 1]) > diff:
A_95 = A_step[j - 2] + 0.5 * dA
else:
A_95 = A_step[j - 1] + 0.5 * dA
print(" Best fit A: {0}".format(exp_A))
print(" error bars: {0}".format(np.sqrt(var_A)))
print(" significance: {0}".format(signif_A))
print(" Chi^2 of fit: {0}".format(
self.chi_sqrd(exp_A, del_z_bar, sep, Cov_mat)))
print(" 95% confidence: {0}".format(A_95))
return exp_A, var_A
def cdf(self, x):
"""
Computes the cumulative distribution function of the
distribution at the point(s) x. The cdf is defined as follows:
F(x|k) = gammainc(k/2, x/2) / gamma(k/2)
Where gammainc and gamma are the incomplete gamma and gamma functions,
respectively.
Parameters
----------
x: array, dtype=float, shape=(m x n)
The value(s) at which the user would like the cdf evaluated.
If an array is passed in, the cdf is evaluated at every point
in the array and an array of the same size is returned.
Returns
-------
cdf: array, dtype=float, shape=(m x n)
The cdf at each point in x.
"""
cdf = chdtr(self.k, x)
return cdf
def cdf(self, x):
"""
Computes the cumulative distribution function of the
distribution at the point(s) x. The cdf is defined as follows:
F(x|k) = gammainc(k/2, x/2) / gamma(k/2)
Where gammainc and gamma are the incomplete gamma and gamma functions,
respectively.
Parameters
----------
x: array, dtype=float, shape=(m x n)
The value(s) at which the user would like the cdf evaluated.
If an array is passed in, the cdf is evaluated at every point
in the array and an array of the same size is returned.
Returns
-------
cdf: array, dtype=float, shape=(m x n)
The cdf at each point in x.
"""
cdf = chdtr(self.k, x)
return cdf
def _cdfchi2(x, df):
return special.chdtr(df, x)
def fit_for_A(self, seps, del_z_bar, N, b_g_rel, c_rel, n, Cov_mat,
covar_type, nbins):
# This is to isolate the n for debugging
i, j = np.indices(Cov_mat.shape)
mod_matrix = np.zeros(Cov_mat.shape)
mod_matrix[np.logical_and(i == j, i >= nbins * (n - 1))] = 1
Cov_mat_I = np.matrix(mod_matrix) * Cov_mat.I * np.matrix(mod_matrix)
# end debugging block
self.c_rel = c_rel
self.get_quad_coeff_for_alpha(b_g_rel, n)
del_z_bar_flat = del_z_bar.flatten()
print(del_z_bar_flat)
A_step, dA = np.linspace(0.,
10.**(2 - n / 2.),
199,
endpoint=True,
retstep=True)
prob_step = np.asarray([
np.exp(-0.5 *
self.chi_sqrd(A_i, del_z_bar_flat, seps, n, Cov_mat_I))
for A_i in A_step
])
prob_step *= 1. / simp_integral(dA, prob_step)
exp_A = simp_integral(dA, prob_step * A_step)
var_A = simp_integral(dA, prob_step * np.power(A_step, 2)) - np.power(
exp_A, 2)
# find max probability A
bi = np.array([0, 10**(2. - n / 2.)])
for i in range(20):
left_chi = self.chi_sqrd(bi[0], del_z_bar_flat, seps, n, Cov_mat)
right_chi = self.chi_sqrd(bi[1], del_z_bar_flat, seps, n, Cov_mat)
if left_chi < right_chi:
bi[1] = np.average(bi)
else:
bi[0] = np.average(bi)
A_min_chi = np.average(bi)
plt.plot(A_step, prob_step)
plt.axvline(x=exp_A, ymin=0, ymax=1, color='k')
plt.axvline(x=exp_A - np.sqrt(var_A),
ymin=0,
ymax=1,
color='k',
linestyle='--')
plt.axvline(x=exp_A + np.sqrt(var_A),
ymin=0,
ymax=1,
color='k',
linestyle='--')
plt.axvline(x=A_min_chi, ymin=0, ymax=1, color='r')
plt.xlabel('A')
plt.ylabel('Probability of fit')
plt.savefig('auto/probability/combined/Prob_A_{0}_{1}.png'.format(
n, covar_type))
plt.close()
CP_A = chdtr(nbins * n - 1,
self.chi_sqrd(0, del_z_bar_flat, seps, n, Cov_mat))
signif_A = np.sqrt(2) * erfinv(CP_A)
j = (np.where(
np.array([
simp_integral(dA, prob_step[:i])
for i in range(3, A_step.size + 1, 2)
]) > 0.95)[0][0] + 1) * 2
diff = 0.95 - simp_integral(dA, prob_step[:j - 1])
if 0.5 * dA * (prob_step[j - 2] + prob_step[j - 1]) > diff:
A_95 = A_step[j - 2] + 0.5 * dA
else:
A_95 = A_step[j - 1] + 0.5 * dA
print(" Best fit A: {0}".format(exp_A))
print(" A with max Prob: {0}".format(A_min_chi))
print(" error bars: {0}".format(np.sqrt(var_A)))
print(" significance: {0}".format(signif_A))
print(" Chi^2 of fit: {0}".format(
self.chi_sqrd(exp_A, del_z_bar_flat, seps, n, Cov_mat)))
print(" 95% confidence: {0}".format(A_95))
return exp_A, var_A
def _cdfchi2(x, df):
return special.chdtr(df, x) # pylint: disable=no-member
def _cdfchi2(x, df):
return special.chdtr(df, x)