def estimate_sigma(observed, df, upper_bound, factor=3, npts=50, nsample=2000):
"""
Produce an estimate of $\sigma$ from a constrained
error sum of squares. The relevant distribution is a
scaled $\chi^2$ restricted to $[0,U]$ where $U$ is `upper_bound`.
Parameters
----------
observed : float
The observed sum of squares.
df : float
Degrees of freedom of the sum of squares.
upper_bound : float
Upper limit of truncation interval.
factor : float
Range of candidate values is
[observed/factor, observed*factor]
npts : int
How many candidate values for interpolator.
nsample : int
How many samples for each expected value
of the truncated sum of squares.
Returns
-------
sigma_hat : np.float
Estimate of $\sigma$.
"""
values = np.linspace(1. / factor, factor, npts) * observed
expected = 0 * values
for i, value in enumerate(values):
P_upper = chidist.cdf(upper_bound * np.sqrt(df) / value, df)
U = np.random.sample(nsample)
sample = chidist.ppf(P_upper * U, df) * value
expected[i] = np.mean(sample**2)
if expected[i] >= 1.1 * (observed**2 * df + observed**2 * df**(0.5)):
break
interpolant = interp1d(values, expected + df**(0.5) * values**2)
V = np.linspace(1. / factor, factor, 10 * npts) * observed
# this solves for the solution to
# expected(sigma) + sqrt(df) * sigma^2 = observed SS * (1 + sqrt(df))
# the usual "MAP" estimator would have RHS just observed SS
# but this factor seems to ``correct it''.
# it is such that if there were no selection it would be
# the usual unbiased estimate
sigma_hat = np.min(
V[interpolant(V) >= observed**2 * df + observed**2 * df**(0.5)])
return sigma_hat
def wald_test(tau, Sigma, alpha=0.05, max_condition=1e-6, pval=False):
"""
Test based on the chi_d distribution.
:param tau: observed test statistics (scaled with sqrt(n)
:param Sigma: observed covariance matrix
:param alpha: level of the test
:param max_condition: determines at which threshold eigenvalues are considered as 0
:param pval: if true, returns the conditional p value instead of the test result
:return: level of the test
"""
# instead of regularizing we preprocess Sigma and tau to get rid of 0 eigenvalues
tau, Sigma = preprocessing(tau, Sigma, max_condition=max_condition)
d = len(tau)
# compute matrix inverse
Sigma_inv = np.linalg.inv(Sigma)
# below quantity is asymptotically standard normal
t_obs = np.sqrt(tau @ Sigma_inv @ tau)
# compute the 1-alpha quantile of the chi distribution with d degrees of freedom
threshold = chi.ppf(q=1-alpha, df=d)
if not pval:
if t_obs > threshold:
return 1
else:
return 0
else:
# return p value
return 1 - chi.cdf(x=t_obs, df=d)
def estimate_sigma(observed, df, upper_bound, factor=3, npts=50, nsample=2000):
"""
Produce an estimate of $\sigma$ from a constrained
error sum of squares. The relevant distribution is a
scaled $\chi^2$ restricted to $[0,U]$ where $U$ is `upper_bound`.
Parameters
----------
observed : float
The observed sum of squares.
df : float
Degrees of freedom of the sum of squares.
upper_bound : float
Upper limit of truncation interval.
factor : float
Range of candidate values is
[observed/factor, observed*factor]
npts : int
How many candidate values for interpolator.
nsample : int
How many samples for each expected value
of the truncated sum of squares.
Returns
-------
sigma_hat : np.float
Estimate of $\sigma$.
"""
values = np.linspace(1./factor, factor, npts) * observed
expected = 0 * values
for i, value in enumerate(values):
P_upper = chidist.cdf(upper_bound * np.sqrt(df) / value, df)
U = np.random.sample(nsample)
sample = chidist.ppf(P_upper * U, df) * value
expected[i] = np.mean(sample**2)
if expected[i] >= 1.1 * (observed**2 * df + observed**2 * df**(0.5)):
break
interpolant = interp1d(values, expected + df**(0.5) * values**2)
V = np.linspace(1./factor,factor,10*npts) * observed
# this solves for the solution to
# expected(sigma) + sqrt(df) * sigma^2 = observed SS * (1 + sqrt(df))
# the usual "MAP" estimator would have RHS just observed SS
# but this factor seems to ``correct it''.
# it is such that if there were no selection it would be
# the usual unbiased estimate
sigma_hat = np.min(V[interpolant(V) >= observed**2 * df + observed**2 * df**(0.5)])
return sigma_hat
def chi_norm(emg_data, params):
emg_data = norm_emg(emg_data)
emg_data = np.abs(emg_data)
#emg_data = norm_emg(emg_data)
for chnl in range(len(emg_data)):
arg = params[chnl][:-2]
loc = params[chnl][-2]
scale = params[chnl][-1]
a_max = chi.ppf(0.9999999999999999, loc=loc, scale=scale, *arg)
a_min = chi.ppf(0.00000000001, loc=loc, scale=scale, *arg)
transf = np.clip(emg_data[chnl, :], a_min=a_min, a_max=a_max)
transf = chi.cdf(transf, loc=loc, scale=scale, *arg)
emg_data[chnl] = norm.ppf(transf)
return emg_data
def grcdf(norm, dim):
"""
Gaussian radial CDF.
@type norm: array_like
@param norm: norms of the data points
@type dim: integer
@param dim: dimensionality of the Gaussian
"""
if dim < 2:
return erf(norm / sqrt(2.))
else:
return chi.cdf(norm, dim)
def grcdf(norm, dim): """ Gaussian radial CDF. @type norm: array_like @param norm: norms of the data points @type dim: integer @param dim: dimensionality of the Gaussian """ if dim < 2: return erf(norm / sqrt(2.)) else: return chi.cdf(norm, dim)
def pStar(M, d, mu, sigma, rho, region, regionNumber, nu, omega):
gamma = sigma(d, rho)
if region == elipsoid:
win = []
for i in range(M):
T = orthoT(d)
v = unitV(d)
inRegion = [2*(math.sqrt(nu)/omega)*np.dot(T, vector).item(0) for vector in v if np.dot(T, vector).item(0) >= 0]
win.append(sum([chi.cdf(value, d) for value in inRegion]))
else:
win = [0]
for i in range(M):
T = orthoT(d)
v = unitV(d)
Tv = [np.dot(T, vector) for vector in v]
for vector in Tv:
if (np.array(np.dot(vector, gamma) * (math.sqrt(nu) / omega)) <= 0).all():
win.append(1)
return sum(win)/(M*len(v))
def test_chi(self):
from scipy.stats import chi
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1, 1)
df = 78
mean, var, skew, kurt = chi.stats(df, moments='mvsk')
x = np.linspace(chi.ppf(0.01, df), chi.ppf(0.99, df), 100)
ax.plot(x, chi.pdf(x, df), 'r-', lw=5, alpha=0.6, label='chi pdf')
rv = chi(df)
ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf')
vals = chi.ppf([0.001, 0.5, 0.999], df)
np.allclose([0.001, 0.5, 0.999], chi.cdf(vals, df))
r = chi.rvs(df, size=1000)
ax.hist(r, density=True, histtype='stepfilled', alpha=0.2)
ax.legend(loc='best', frameon=False)
self.assertEqual(str(ax), "AxesSubplot(0.125,0.11;0.775x0.77)")
def estimate_sigma(observed, truncated_df, lower_bound, upper_bound, untruncated_df=0, factor=3, npts=50, nsample=2000):
"""
Produce an estimate of $\sigma$ from a constrained
error sum of squares. The relevant distribution is a
scaled $\chi^2$ restricted to $[0,U]$ where $U$ is `upper_bound`.
Parameters
----------
observed : float
The observed sum of squares.
truncated_df : float
Degrees of freedom of the truncated $\chi^2$ in the sum of squares.
The observed sum is assumed to be the sum
of an independent untruncated $\chi^2$ and the truncated one.
lower_bound : float
Lower limit of truncation interval.
upper_bound : float
Upper limit of truncation interval.
untruncated_df : float
Degrees of freedom of the untruncated $\chi^2$ in the sum of squares.
factor : float
Range of candidate values is
[observed/factor, observed*factor]
npts : int
How many candidate values for interpolator.
nsample : int
How many samples for each expected value
of the truncated sum of squares.
Returns
-------
sigma_hat : np.float
Estimate of $\sigma$.
"""
if untruncated_df < 50:
linear_term = truncated_df**(0.5)
else:
linear_term = 0
total_df = untruncated_df + truncated_df
values = np.linspace(1./factor, factor, npts) * observed
expected = 0 * values
for i, value in enumerate(values):
P_upper = chidist.cdf(upper_bound * np.sqrt(truncated_df) / value, truncated_df)
P_lower = chidist.cdf(lower_bound * np.sqrt(truncated_df) / value, truncated_df)
U = np.random.sample(nsample)
if untruncated_df > 0:
sample = (chidist.ppf((P_upper - P_lower) * U + P_lower, truncated_df)**2 + chidist.rvs(untruncated_df, size=nsample)**2) * value**2
else:
sample = (chidist.ppf((P_upper - P_lower) * U + P_lower, truncated_df) * value)**2
expected[i] = np.mean(sample)
if expected[i] >= 1.5 * (observed**2 * total_df + observed**2 * linear_term):
break
interpolant = interp1d(values, expected + values**2 * linear_term)
V = np.linspace(1./factor,factor,10*npts) * observed
# this solves for the solution to
# expected(sigma) + sqrt(df) * sigma^2 = observed SS * (1 + sqrt(df))
# the usual "MAP" estimator would have RHS just observed SS
# but this factor seems to correct it.
# it is such that if there were no selection it would be
# the usual unbiased estimate
try:
sigma_hat = np.min(V[interpolant(V) >= observed**2 * total_df + observed**2 * linear_term])
except ValueError:
# no solution, just return observed
sigma_hat = observed
return sigma_hat
def grcdf(norm, dim): """ Gaussian radial CDF. """ return chi.cdf(norm, dim)
data_path = r'C:\Users\win10\Desktop\Projects\CYB\Experiment_Balint\CYB005\Data'
n_channels = 8
X = np.empty((n_channels, 0))
for i, file in enumerate(
sorted([f for f in os.listdir(data_path) if f.endswith('.json')])):
with open(data_path + '\\' + file) as json_file:
dict_data = json.load(json_file)
X = np.concatenate((X, dict_data["EMG"]), axis=1)
if i >= 9:
break
print("Loaded")
data = X[0, :]
data = (data - np.mean(data)) / np.std(data)
data = np.abs(data[abs(data - np.mean(data)) < 4 * np.std(data)])
params = chi.fit(data)
# Separate parts of parameters
arg = params[:-2]
loc = params[-2]
scale = params[-1]
# Calculate fitted PDF and error with fit in distribution
transf = chi.cdf(data, loc=loc, scale=scale, *arg)
transf = norm.ppf(transf)
plt.figure()
plt.hist(transf, bins=50)
plt.show()
Y_j = B_j_prime.T.dot(C_pca_vec)
# project C to PCA
Z_j = C_j_prime.dot(C_pca_vec)
# Step 3a: standarlization of anomalies
Z_j_sd = Z_j.std(axis=0)
X_prime = X/Z_j_sd
Y_j_prime = Y_j/Z_j_sd
for int_loop in range(0, len(dist_id_sel)):
# (v2.5 insert C_eigen_val_count as the PCs truncation threshold)
distances[int_loop, ref_dist] = np.linalg.norm(
X_prime[int_loop, 0:C_eigen_val_count]-Y_j_prime[0:C_eigen_val_count])
print(ref_dist, int_loop, B_ctrl, mdl_c)
mdl_c_disp = str(B_ctrl+1)
locals()[mdl+"_distance_vals_B"+mdl_c_disp] = distances
locals()[mdl+"_distance_pct_B" +
mdl_c_disp] = chi.cdf(distances, C_eigen_val_count)
percents = locals()[mdl+"_distance_pct_B"+mdl_c_disp]
to_excl_vals = pd.DataFrame(distances)
to_excl_vals.to_excel(excel_writer=mdl+"_B"+mdl_c_disp+"_vals.xlsx")
to_excl_pct = pd.DataFrame(locals()[mdl+"_distance_pct_B"+mdl_c_disp])
to_excl_pct.to_excel(excel_writer=mdl+"_B"+mdl_c_disp+"_pct.xlsx")
min_dist_val = np.amin(distances, axis=0)
min_dist_ind = []
for min_ind in range(0, min_dist_val.shape[0]):
xt = [act for act in percents[:, min_ind] if act <= 0.68]
xt_where = np.where(percents[:, min_ind] <= 0.68)
analog_ct = len(xt)
dist_space = []
dist_space_id = []
if analog_ct == 0:
print("no analog, all novel climates", file=f_c_d_na)
def ost_test(tau,
Sigma,
alpha=0.05,
selection='discrete',
max_condition=1e-6,
accuracy=1e-6,
constraints='Sigma',
pval=False):
"""
Runs the full test suggested in our paper.
:param tau: observed statistic
:param Sigma: covariance matrix
:param alpha: level of test
:param selection: continuous/discrete (discrete is not extensively tested)
:param max_condition: at which condition number the covariance matrix is truncated.
:param accuracy: threshold to determine whether an entry is zero
:param constraints: if 'Sigma' we work with the constraints (Sigma beta) >=0. If 'positive' we work with beta >= 0
:param pval: if true, returns the conditional p value instead of the test result
:return: 1 (reject), 0 (no reject)
"""
assert constraints == 'Sigma' or constraints == 'positive', 'Constraints are not implemented'
# if the selection is discrete we dont want any transformations
if selection == 'discrete':
constraints = 'positive'
# check if there are entries with 0 variance
zeros = [i for i in range(len(tau)) if Sigma[i][i] < 1e-10]
tau = np.delete(tau, zeros)
Sigma = np.delete(Sigma, zeros, 0)
Sigma = np.delete(Sigma, zeros, 1)
if constraints == 'Sigma':
# compute pseudoinverse to also handle singular covariances (see Appendix)
r_cond = max_condition # parameter which precision to use
Sigma_inv = np.linalg.pinv(Sigma, rcond=r_cond, hermitian=True)
# use Remark 1 to convert the problem
tau = Sigma_inv @ tau
Sigma = Sigma_inv
# Apply Theorem 1 in the canonical form with beta>=0 constraints
beta_star = optimization(tau=tau, Sigma=Sigma, selection=selection)
# determine active set
non_zero = [1 if beta_i > accuracy else 0 for beta_i in beta_star]
projector = np.diag(non_zero)
effective_sigma = projector @ Sigma @ projector
# Use the rank of effective Sigma to determine how many degrees of freedom the covariance has after conditioning
# for non-singular original covariance, this is the same number as the number of active dimensions |mathcal{U}|,
# however, for singular cases using the rank is the right way to go.
tol = max_condition * np.max(np.linalg.eigvalsh(Sigma))
r = np.linalg.matrix_rank(effective_sigma, tol=tol, hermitian=True)
# go back to notation used in the paper
l = r
if l > 1:
test_statistic = beta_star @ tau / np.sqrt(
beta_star @ Sigma @ beta_star)
threshold = chi_stats.ppf(q=1 - alpha, df=l)
else:
vminus = truncation(beta_star=beta_star,
tau=tau,
Sigma=Sigma,
accuracy=accuracy)
threshold = truncated_gaussian(var=beta_star @ Sigma @ beta_star,
v_minus=vminus,
level=alpha)
test_statistic = beta_star @ tau
if not pval:
if test_statistic > threshold:
# reject
return 1
else:
# cannot reject
return 0
if pval:
if l > 1:
test_statistic = beta_star @ tau / np.sqrt(
beta_star @ Sigma @ beta_star)
pvalue = 1 - chi_stats.cdf(x=test_statistic, df=l)
else:
test_statistic = beta_star @ tau / np.sqrt(
beta_star @ Sigma @ beta_star)
vminus = truncation(beta_star=beta_star, tau=tau, Sigma=Sigma, accuracy=accuracy) / \
np.sqrt(beta_star @ Sigma @ beta_star)
pvalue = 1 - (norm.cdf(x=test_statistic) -
norm.cdf(x=vminus)) / (1 - norm.cdf(x=vminus))
return pvalue
def grcdf(norm, dim):
"""
Gaussian radial CDF.
"""
return chi.cdf(norm, dim)
def chi_pvalue(observed, lower_bound, upper_bound, sd, df, method='MC', nsim=1000):
r"""
Compute a truncated $\chi$ p-value based on the
conditional survival function.
Parameters
----------
observed : float
lower_bound : float
upper_bound : float
sd : float
Standard deviation.
df : float
Degrees of freedom.
method: string
One of ['MC', 'cdf', 'sf']
Returns
-------
pvalue : float
Notes
-----
Let $T$ be `observed`, $L$ be `lower_bound` and $U$ be `upper_bound`,
and $\sigma$ be `sd`.
The p-value, for $L \leq T \leq U$ is
.. math::
\frac{P(\chi^2_k / \sigma^2 \geq T^2) - P(\chi^2_k / \sigma^2 \geq U^2)}
{P(\chi^2_k / \sigma^2 \geq L^2) - P(\chi^2_k / \sigma^2 \geq U^2)}
It can be computed using `scipy.stats.chi` either its `cdf` (distribution
function) or `sf` (survival function) or evaluated
by Monte Carlo if method is `MC`.
"""
L, T, U = lower_bound, observed, upper_bound # shorthand
if method == 'cdf':
pval = ((chi.cdf(U / sd, df) - chi.cdf(T / sd, df)) /
(chi.cdf(U / sd, df) - chi.cdf(L / sd, df)))
elif method == 'sf':
pval = ((chi.sf(U / sd, df) - chi.sf(T / sd, df)) /
(chi.sf(U / sd, df) - chi.sf(L / sd, df)))
elif method == 'MC':
if df == 1:
H = []
else:
H = [0]*(df-1)
pval = general_pvalue(T / sd, L / sd, U / sd, H, nsim=nsim)
else:
raise ValueError('method should be one of ["cdf", "sf", "MC"]')
if pval == 1: # the distribution functions may have failed -- use MC
pval = general_pvalue(T / sd, L / sd, U / sd, H, nsim=50000)
if pval > 1:
pval = 1
return pval
for i, ecdf in enumerate(params):
axes.flatten()[i].hist(X1[i, :],
bins=100,
density=True,
rwidth=1,
edgecolor=sns.color_palette()[0])
if i % 2 is 0:
axes.flatten()[i].set_ylabel("Probability density")
if i > 5:
axes.flatten()[i].set_xlabel("Normalised voltage")
plt.tight_layout()
plt.show()
plt.show()
print(chi.cdf(8.47, loc=params[6][-2], scale=params[6][-1], *params[6][:-2]))
# Display
n_channels = 8
X = np.empty((n_channels, 0))
for file in sorted([f for f in os.listdir(data_path) if f.endswith('.json')]):
with open(data_path + '\\' + file) as json_file:
dict_data = json.load(json_file)
emg_data = np.array(dict_data["EMG"])
X = np.hstack((X, emg_data))
X_std = np.std(X, axis=1)
X_mean = np.mean(X, axis=1)
X = (X - X_mean[:, None]) / X_std[:, None]
params = list()
dist = chi
for chnl in range(len(X)):
Y_j = B_j_prime.T.dot(C_pca_vec)
# project C to PCA
Z_j = C_j_prime.dot(C_pca_vec)
## Step 3a: standarlization of anomalies
Z_j_sd = Z_j.std(axis=0)
X_prime = X / Z_j_sd
Y_j_prime = Y_j / Z_j_sd
for int_loop in range(0, len(dist_id_sel)):
# (v2.5 insert C_eigen_val_count as the PCs truncation threshold)
distances[int_loop, ref_dist] = np.linalg.norm(
X_prime[int_loop, 0:C_eigen_val_count] -
Y_j_prime[0:C_eigen_val_count])
print(ref_dist, int_loop, B_ctrl, mdl_c)
mdl_c_disp = str(B_ctrl + 1)
locals()[mdl + "_distance_vals_B" + mdl_c_disp] = distances
locals()[mdl + "_distance_pct_B" + mdl_c_disp] = chi.cdf(
distances, C_eigen_val_count)
percents = locals()[mdl + "_distance_pct_B" + mdl_c_disp]
to_excl_vals = pd.DataFrame(distances)
to_excl_vals.to_excel(excel_writer=mdl + "_B" + mdl_c_disp +
"_vals.xlsx")
to_excl_pct = pd.DataFrame(locals()[mdl + "_distance_pct_B" +
mdl_c_disp])
to_excl_pct.to_excel(excel_writer=mdl + "_B" + mdl_c_disp +
"_pct.xlsx")
min_dist_val = np.amin(distances, axis=0)
min_dist_ind = []
for min_ind in range(0, min_dist_val.shape[0]):
xt = [act for act in percents[:, min_ind] if act <= 0.68]
xt_where = np.where(percents[:, min_ind] <= 0.68)
map_plotting(ftr=min_ind, alg=xt_where[0])
analog_ct = len(xt)
def get_bin_prob(k, r_grid):
cdf = chi.cdf(r_grid, df=k)
bin_prob = np.diff(cdf)
return bin_prob
# Display the probability density function (``pdf``): x = np.linspace(chi.ppf(0.01, df), chi.ppf(0.99, df), 100) ax.plot(x, chi.pdf(x, df), 'r-', lw=5, alpha=0.6, label='chi pdf') # Alternatively, the distribution object can be called (as a function) # to fix the shape, location and scale parameters. This returns a "frozen" # RV object holding the given parameters fixed. # Freeze the distribution and display the frozen ``pdf``: rv = chi(df) ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf') # Check accuracy of ``cdf`` and ``ppf``: vals = chi.ppf([0.001, 0.5, 0.999], df) np.allclose([0.001, 0.5, 0.999], chi.cdf(vals, df)) # True # Generate random numbers: r = chi.rvs(df, size=1000) # And compare the histogram: ax.hist(r, normed=True, histtype='stepfilled', alpha=0.2) ax.legend(loc='best', frameon=False) plt.show()