def raise_res(T, W, c, mu=0, sigma=1):
"""Increase the resolution of a wiener series by a factor of c.
Returns a more reolved Wiener series and its associate time series
T = the given Time series.
W = the associated Wiener series.
c = Scaling factor (integer greater than 1).
mu = Mean of W's underlying normal distribution.
sigma = Standard deviation of W's underlying normal distribution.
"""
dT = T[1] - T[0]
dt = float(T[1] - T[0]) / c
t_series = []
w_series = []
for i in range(len(T) - 1):
t = T[i]
w_t = W[i]
t_next = T[i + 1]
w_next = W[i + 1]
t_series.append(t)
w_series.append(w_t)
for j in range(c - 1):
t += dt
dW = w_next - w_t
drawfrm_cum = np.sqrt(2) * np.sqrt(t_next - t) * sigma * erfc(random())
if np.sqrt(2) * np.sqrt(t_next - t) * sigma * erfc(-2 * random()) < abs(dW):
w_t += abs(gauss(0, np.sqrt(dt) * sigma)) * float(dW) / abs(dW)
else:
w_t += gauss(0, np.sqrt(dt) * sigma)
t_series.append(t)
w_series.append(w_t)
t_series.append(T[-1])
w_series.append(W[-1])
return t_series, w_series
def truncatedgaussian_sample(xmin, xmax, mu, sigma, x):
roottwo = 1.414213562373095
temp = math.erfc((-xmin + mu) / (roottwo * sigma)) + x * (
math.erfc((-xmax + mu) / (roottwo * sigma)) - math.erfc((-xmin + mu) / (roottwo * sigma))
)
y = mu + roottwo * sigma * coolmath.inverf(-1.0 + temp)
return y
def test_erfc(self):
import math
assert math.erfc(0.0) == 1.0
assert math.erfc(-0.0) == 1.0
assert math.erfc(float("inf")) == 0.0
assert math.erfc(float("-inf")) == 2.0
assert math.isnan(math.erf(float("nan")))
assert math.erfc(1e-308) == 1.0
def test_erfc():
table = [
(0.0, 1.0000000),
(0.05, 0.9436280),
(0.1, 0.8875371),
(0.15, 0.8320040),
(0.2, 0.7772974),
(0.25, 0.7236736),
(0.3, 0.6713732),
(0.35, 0.6206179),
(0.4, 0.5716076),
(0.45, 0.5245183),
(0.5, 0.4795001),
(0.55, 0.4366766),
(0.6, 0.3961439),
(0.65, 0.3579707),
(0.7, 0.3221988),
(0.75, 0.2888444),
(0.8, 0.2578990),
(0.85, 0.2293319),
(0.9, 0.2030918),
(0.95, 0.1791092),
(1.0, 0.1572992),
(1.1, 0.1197949),
(1.2, 0.0896860),
(1.3, 0.0659921),
(1.4, 0.0477149),
(1.5, 0.0338949),
(1.6, 0.0236516),
(1.7, 0.0162095),
(1.8, 0.0109095),
(1.9, 0.0072096),
(2.0, 0.0046777),
(2.1, 0.0029795),
(2.2, 0.0018628),
(2.3, 0.0011432),
(2.4, 0.0006885),
(2.5, 0.0004070),
(2.6, 0.0002360),
(2.7, 0.0001343),
(2.8, 0.0000750),
(2.9, 0.0000411),
(3.0, 0.0000221),
(3.1, 0.0000116),
(3.2, 0.0000060),
(3.3, 0.0000031),
(3.4, 0.0000015),
(3.5, 0.0000007),
(4.0, 0.0000000),
]
for x, y in table:
AlmostEqual(y, math.erfc(x), tolerance=7)
AlmostEqual(2.0 - y, math.erfc(-x), tolerance=7)
def RandIntVec(self,ListSize, ListSumValue, Distribution='Normal'):
"""
Inputs:
ListSize = the size of the list to return
ListSumValue = The sum of list values
Distribution = can be 'uniform' for uniform distribution, 'normal' for a normal distribution ~ N(0,1) with +/- 3 sigma (default), or a list of size 'ListSize' or 'ListSize - 1' for an empirical (arbitrary) distribution. Probabilities of each of the p different outcomes. These should sum to 1 (however, the last element is always assumed to account for the remaining probability, as long as sum(pvals[:-1]) <= 1).
Output:
A list of random integers of length 'ListSize' whose sum is 'ListSumValue'.
"""
if type(Distribution) == list:
DistributionSize = len(Distribution)
if ListSize == DistributionSize or (ListSize-1) == DistributionSize:
Values = multinomial(ListSumValue,Distribution,size=1)
OutputValue = Values[0]
elif Distribution.lower() == 'uniform': #I do not recommend this!!!! I see that it is not as random (at least on my computer) as I had hoped
UniformDistro = [1/ListSize for i in range(ListSize)]
Values = multinomial(ListSumValue,UniformDistro,size=1)
OutputValue = Values[0]
elif Distribution.lower() == 'normal':
"""
Normal Distribution Construction....It's very flexible and hideous
Assume a +-3 sigma range. Warning, this may or may not be a suitable range for your implementation!
If one wishes to explore a different range, then changes the LowSigma and HighSigma values
"""
LowSigma = -3#-3 sigma
HighSigma = 3#+3 sigma
if (float(ListSize) - 1) == 0:
StepSize = 0
else:
StepSize = 1/(float(ListSize) - 1)
ZValues = [(LowSigma * (1-i*StepSize) +(i*StepSize)*HighSigma) for i in range(int(ListSize))]
#Construction parameters for N(Mean,Variance) - Default is N(0,1)
Mean = 0
Var = 1
#NormalDistro= [self.NormalDistributionFunction(Mean, Var, x) for x in ZValues]
NormalDistro= list()
for i in range(len(ZValues)):
if i==0:
ERFCVAL = 0.5 * math.erfc(-ZValues[i]/math.sqrt(2))
NormalDistro.append(ERFCVAL)
elif i == len(ZValues) - 1:
ERFCVAL = NormalDistro[0]
NormalDistro.append(ERFCVAL)
else:
ERFCVAL1 = 0.5 * math.erfc(-ZValues[i]/math.sqrt(2))
ERFCVAL2 = 0.5 * math.erfc(-ZValues[i-1]/math.sqrt(2))
ERFCVAL = ERFCVAL1 - ERFCVAL2
NormalDistro.append(ERFCVAL)
#print "Normal Distribution sum = %f"%sum(NormalDistro)
Values = multinomial(ListSumValue,NormalDistro,size=1)
OutputValue = Values[0]
else:
raise ValueError ('Cannot create desired vector')
return OutputValue
def de_marsily_no_reaction(self,x,t):
# Based on Equation 10.3.2 in Quantitative Hydrogeology, Ghislain de
# Marsily, 1986.
D_ = self.D
U_over_porR = self.U/(self.porosity*self.R)
two_sqrt_Dt_over_porR = 2.*math.sqrt(D_*t/(self.porosity*self.R))
temp = 0.5* \
(math.erfc((x-t*U_over_porR)/two_sqrt_Dt_over_porR) + \
math.exp(self.U*x/D_) * \
math.erfc((x+t*U_over_porR)/two_sqrt_Dt_over_porR))
value = temp*(self.c1-self.c0) + self.c0
return value
def ogata_banks(self,x,t):
# Based on "Solution of the Differential Equation of Longitudinal
# Dispersion in Porous Media", USGS Professional Paper 411-A by
# Akio Ogata and R.B. Banks, 1961.
D_ = self.D/self.porosity
v = self.U/self.porosity
temp = 0.5* \
(math.erfc((x-v/self.R*t)/(2.*math.sqrt(D_/self.R*t))) + \
math.exp(v*x/D_) * \
math.erfc((x+v/self.R*t)/(2.*math.sqrt(D_/self.R*t))))
value = temp*(self.c1-self.c0) + self.c0
return value
def getnormcdf(x,lowertail=True):
"""
Get the normal CDF function. used to calculate p-value
"""
# ax=math.fabs(x)
#axv=math.erfc(x/(2**0.5))/2; # higher tail
if lowertail==False:
#return axv
return math.erfc(x/(2**0.5))/2
else:
#return 1-axv
return math.erfc(-x/(2**0.5))/2
def blackscholes(stockprice, strike, riskfree, time, volatility): d1 = (log(stockprice/strike)+(riskfree+.5*volatility**2)*time)/(volatility*sqrt(time)) d2 = d1 - volatility*sqrt(time) callprice = stockprice*.5*erfc(-d1/sqrt(2))-strike*exp(-riskfree*time)*.5*erfc(-d2/sqrt(2)) putprice = strike*exp(-riskfree*time)*.5*erfc(d2/sqrt(2))-stockprice*.5*erfc(d1/sqrt(2)) calldelta = .5*erfc(-d1/sqrt(2)) putdelta = calldelta - 1 return [callprice, putprice, calldelta, putdelta]
def calculate_results(representedPalindromes, kmer_counts,
totalCharCount, hypothesesCount):
"""
INPUT:
representedPalindromes - A collections.Counter()
object
kmer_counts - A collections.Counter() object.
totalCharCount - An integer
hypothesesCount - An integer
OUTPUT:
tupleList - A list of tuples, each tuple
contains the palindrome name, observed count,
expected count, z-score and E-value.
Takes in a collections.Counter representedPalindromes,
a collections.Counter kmer_counts,
an int totalCharCount, and an int hypothesesCount. For
each palindrome in representedPalindromes the expected
value, z-Score, and e-value is calculated. These three
values are coupled with the palindrome name and observed
count, to create a tuple with five elements. These
tuples are loaded into a list, which is returned after
all palindromes in representedPalindromes has been
iterated over.
"""
tupleList = []
# The list of tuples. Each element in this list is a
# tuple, with five elements. The tuple elements
# are palindrome name, observed count, expected count,
# z-score and E-value.
for key, value in representedPalindromes.items():
if (len(key)%2) == 1:
keyList = list(key)
if(keyList[len(key)/2]) in "ATCG": continue
# Throw out odd palindromes with middle characters
# ATCG, they are not desired.
expectedValue = expected_value(key,kmer_counts)
standardDeviation = (math.sqrt(expectedValue *
(1 - (expectedValue/ totalCharCount))))
zScore = ((kmer_counts[key] - expectedValue)
/standardDeviation)
if zScore <= 0:
e_Value = ((math.erfc(-zScore/math.sqrt(2))/2)*
2*hypothesesCount)
else:
e_Value = ((math.erfc(zScore/math.sqrt(2))/2)
*2*hypothesesCount)
tupleList.append((key, str(value), str(expectedValue),
zScore, e_Value))
return tupleList
def compute_kullback_leibler_check_statistic(n=100, prngstate=None):
"""Compute the lowest of the survival function and the CDF of the exact KL
divergence KL(N(mu1,s1)||N(mu2,s2)) w.r.t. the sample distribution of the
KL divergence drawn by computing log(P(x|N(mu1,s1)))-log(P(x|N(mu2,s2)))
over a sample x~N(mu1,s1). If we are computing the KL divergence
accurately, the exact value should fall squarely in the sample, and the
tail probabilities should be relatively large.
"""
if prngstate is None:
raise TypeError('Must explicitly specify numpy.random.RandomState')
mu1 = mu2 = 0
s1 = 1
s2 = 2
exact = gaussian_kl_divergence(mu1, s1, mu2, s2)
sample = prngstate.normal(mu1, s1, n)
lpdf1 = gaussian_log_pdf(mu1, s1)
lpdf2 = gaussian_log_pdf(mu2, s2)
estimate, std = kl.kullback_leibler(sample, lpdf1, lpdf2)
# This computes the minimum of the left and right tail probabilities of the
# exact KL divergence vs a gaussian fit to the sample estimate. There is a
# distinct negative skew to the samples used to compute `estimate`, so this
# statistic is not uniform. Nonetheless, we do not expect it to get too
# small.
return erfc(abs(exact - estimate) / std) / 2
def F8_f(self):
self.F8 = 0.5 * math.erfc(-self.z_score/math.sqrt(2))
if self.F8 == 0:
self.F8 = 10^-16
else:
self.F8 = self.F8
return self.F8
def Ea(self,n_1,r):
'''
This function computes Easiness of task dependent on Reaction Time and Accuracy
Arguments:
n_1 - One of the numerical numbers in the task
r - Ratio of numbers in the task
In order to compute the P_Error an erfc formula consisting of the two numbers and the weber fraction is used
'''
m = (self.m)
intercept = self.i
w = self.w
dist = int(round(n_1 / r)) - n_1
rt = (dist * m) + intercept # Computing Reaction_Time from the values obtained from the RT graph
n_2 = int(round(n_1/r))
numer = abs(n_1-n_2)
denom = math.sqrt(2)*w*(((n_1**2)+(n_2**2))**0.5)
P_Err = 0.5*math.erfc(numer/denom)
P_A = 1 - P_Err
#print(P_A)
array_poss = np.random.choice([0,1],size=(10),p=[1-P_A, P_A]) # Generating bin values array (consisting of 0's and 1's)using P_Acc probability
val = np.random.choice(array_poss) # Randomly choosing samples from array_poss
rt = np.random.normal(rt,intercept) # Normal Distribution sampling of RT vals
if rt<500:
rt = 500 # re-evaluate RT's < 500
rt = np.random.normal(rt,130)
E = val - (rt/2000.) # Computing discrete Easiness value of a question
return E, val, rt
def _calc_real_and_point(self):
"""
Determines the self energy -(eta/pi)**(1/2) * sum_{i=1}^{N} q_i**2
If cell is charged a compensating background is added (i.e. a G=0 term)
"""
all_nn = self._s.get_all_neighbors(self._rmax, True)
forcepf = 2.0 * self._sqrt_eta / sqrt(pi)
coords = self._coords
numsites = self._s.num_sites
ereal = np.zeros((numsites, numsites))
epoint = np.zeros((numsites))
forces = np.zeros((numsites, 3))
for i in xrange(numsites):
nn = all_nn[i] #self._s.get_neighbors(site, self._rmax)
qi = self._oxi_states[i]
epoint[i] = qi * qi
epoint[i] *= -1.0 * sqrt(self._eta / pi)
epoint[i] += qi * pi / (2.0 * self._vol * self._eta) #add jellium term
for j in range(len(nn)): #for (nsite, rij) in nn:
nsite = nn[j][0]
rij = nn[j][1]
qj = compute_average_oxidation_state(nsite)
erfcval = erfc(self._sqrt_eta * rij)
ereal[nn[j][2], i] += erfcval * qi * qj / rij
fijpf = qj / pow(rij, 3) * (erfcval + forcepf * rij * exp(-self._eta * pow(rij, 2)))
forces[i] += fijpf * (coords[i] - nsite.coords) * qi * EwaldSummation.CONV_FACT
ereal = ereal * 0.5 * EwaldSummation.CONV_FACT
epoint = epoint * EwaldSummation.CONV_FACT
return (ereal, epoint, forces)
def graph_FWHM_data_range(start_date=datetime.datetime(2015,3,6),
end_date=datetime.datetime(2015,4,15),tenmin=True,
path='/home/douglas/Dropbox (Thacher)/Observatory/Seeing/Data/',
write=True,outpath='./'):
plot_params()
fwhm = get_FWHM_data_range(start_date = start_date, end_date=end_date, path=path, tenmin=tenmin)
# Basic stats
med = np.median(fwhm)
mean = np.mean(fwhm)
fwhm_clip, low, high = sigmaclip(fwhm,low=3,high=3)
meanclip = np.mean(fwhm_clip)
# Get mode using kernel density estimation (KDE)
vals = np.linspace(0,30,1000)
fkde = gaussian_kde(fwhm)
fpdf = fkde(vals)
mode = vals[np.argmax(fpdf)]
std = np.std(fwhm)
plt.ion()
plt.figure(99)
plt.clf()
plt.hist(fwhm, color='darkgoldenrod',bins=35)
plt.xlabel('FWHM (arcsec)',fontsize=16)
plt.ylabel('Frequency',fontsize=16)
plt.annotate('mode $=$ %.2f" ' % mode, [0.87,0.85],horizontalalignment='right',
xycoords='figure fraction',fontsize='large')
plt.annotate('median $=$ %.2f" ' % med, [0.87,0.8],horizontalalignment='right',
xycoords='figure fraction',fontsize='large')
plt.annotate('mean $=$ %.2f" ' % mean, [0.87,0.75],horizontalalignment='right',
xycoords='figure fraction',fontsize='large')
xvals = np.linspace(0,30,1000)
kde = gaussian_kde(fwhm)
pdf = kde(xvals)
dist_c = np.cumsum(pdf)/np.sum(pdf)
func = interp1d(dist_c,vals,kind='linear')
lo = np.float(func(math.erfc(1./np.sqrt(2))))
hi = np.float(func(math.erf(1./np.sqrt(2))))
disthi = np.linspace(.684,.999,100)
distlo = disthi-0.6827
disthis = func(disthi)
distlos = func(distlo)
interval = np.min(disthis-distlos)
plt.annotate('1 $\sigma$ int. $=$ %.2f" ' % interval, [0.87,0.70],horizontalalignment='right',
xycoords='figure fraction',fontsize='large')
plt.rcdefaults()
plt.savefig(outpath+'Seeing_Cumulative.png',dpi=300)
return
def bear(self,x,t):
# Based on Equation 10.6.22 in "Dynamics of Fluids in Porous Media",
# Jacob Bear, 1988.
D_ = self.D/self.porosity
v = self.U/self.porosity
beta = math.sqrt(v*v/(4.*D_*D_)+ self.lam/D_)
temp = 0.5 * \
math.exp(v*x/(2.*D_)) * \
(math.exp(-1.*beta*x) * \
math.erfc((x-math.sqrt(v*v+4.*self.lam*D_)*t) / \
(2.*math.sqrt(D_*t))) + \
math.exp(beta*x) * \
math.erfc((x+math.sqrt(v*v+4.*self.lam*D_)*t) / \
(2.*math.sqrt(D_*t))))
value = temp*(self.c1-self.c0) + self.c0
return value
def monobit(bits):
ceros= bits.count("0")
unos = bits.count("1")
frequencia = len(bits)
SN = ceros-unos
test = abs(SN)/sqrt(frequencia)
return erfc(test/sqrt(2))
def rspace_sum(rs, qs, basis, kappa, rlim):
"""
Real space part of the sum
Parameters:
rs -- list of particle positions
qs -- list of particle charges
basis -- real space basis
kappa -- splitting parameter
rlim -- size of lattice (one side of a cube of points)
"""
rspace_sum = 0.0
for i in range(len(rs)):
for j in range(len(rs)):
q = qs[i]*qs[j]
r = rs[j] - rs[i]
for n1 in range(-rlim+1, rlim):
for n2 in range(-rlim+1, rlim):
for n3 in range(-rlim+1, rlim):
if i == j and n1 == 0 and n2 == 0 and n3 == 0:
continue
lat = n1*basis[0] + n2*basis[1] + n3*basis[2]
d = r + lat
rd = math.sqrt(d.dot(d))
rspace_sum += q * math.erfc(kappa*rd)/rd
return rspace_sum
def distparams(dist):
"""
Description:
------------
Return robust statistics of a distribution of data values
Example:
--------
med,mode,interval,lo,hi = distparams(dist)
"""
from scipy.stats.kde import gaussian_kde
from scipy.interpolate import interp1d
vals = np.linspace(np.min(dist)*0.5,np.max(dist)*1.5,1000)
kde = gaussian_kde(dist)
pdf = kde(vals)
dist_c = np.cumsum(pdf)/np.sum(pdf)
func = interp1d(dist_c,vals,kind='linear')
lo = np.float(func(math.erfc(1./np.sqrt(2))))
hi = np.float(func(math.erf(1./np.sqrt(2))))
med = np.float(func(0.5))
mode = vals[np.argmax(pdf)]
disthi = np.linspace(.684,.999,100)
distlo = disthi-0.6827
disthis = func(disthi)
distlos = func(distlo)
interval = np.min(disthis-distlos)
return med,mode,interval,lo,hi
def TraditionalEwald(L,D,rs,nMax):
alpha = 7./(L)
VShort = lambda r,a: math.erfc(a*r)/r
fVLong = lambda k2,a: 4*pi*math.exp(-k2/(4*a*a))/(k2*(L**D))
# Short-ranged r-space
Vss = []
for r in rs:
Vs = VShort(r,alpha)
Vss.append(Vs)
# Long-ranged k-space
ns = Genns(nMax,D)
ks = []
fVls = []
for n in ns:
magn2 = dot(n,n)
k2 = 4.*pi*pi*magn2/(L*L)
ks.append(math.sqrt(k2))
if magn2 != 0:
fVl = fVLong(k2,alpha)
fVls.append(fVl)
else:
fVls.append(0.)
ks, fVls = GetUnique(ks,fVls)
for (k,fVl) in sorted(zip(ks,fVls)):
print k, fVl
return [Vss,fVls]
def monobit (bits, p_value=0.01):
"""Monobit Test
returns a tuple representing (metric, pass)"""
S = bits.count(1) - bits.count(0)
S_obs = abs(S) / math.sqrt(len(bits))
P = math.erfc(S_obs / math.sqrt(2))
return P, P >= p_value
def phi(sigma):
# sigma is your standard deviation
# sigma = 3.0
# 4.891639 sigma is (basically) 1 in a million
sampleSize = (1./ (math.erfc(sigma/sqrt(2))))
# "80 billion 'events' in an day at Intel..."
msg = '1 in a', sampleSize, 'or ', 80e9/sampleSize, ' for an IntelDay'
return (print(msg))
def levyCDF(x, mu = 0, sigma = 0.5):
F = []
for num in range(0, len(x)):
temp = math.sqrt(sigma / (2*(x[num] - mu)))
F.append(math.erfc(temp))
return F
def runs_test2 (bits, p_value=0.01):
"""Custom Runs Test (pi = 0.5)
returns a tuple representing (metric, pass)"""
n = len(bits)
pi = .5
vobs = (bits[0:n-1] ^ bits[1:n]).count(1) + 1
pval = math.erfc(abs(vobs-2*n*pi*(1-pi)) / (2 * math.sqrt(2*n) * pi * (1 - pi)))
return pval, pval >= p_value
def frequency_test(bsq):
bsqc = [ 2*x -1 for x in bsq ]
n = len(bsq)
s_obs = abs(sum(bsqc)) / sqrt(float(n))
p_value = erfc(s_obs/sqrt(2))
reason = "There is a disproportion between the number of 0 and 1:\n"
reason += "#0: {} #1: {}".format(bsq.count(0), bsq.count(1))
return p_value, reason
def lognorm_cdf(x, mean, var):
""" cumulative distribution function of a log-normal distribution
parameterized by its `mean` and variance `var` """
mean2 = mean**2
return 0.5 * math.erfc(
np.log(mean2 / (x*np.sqrt(mean2 + var))) /
(np.sqrt(2 * np.log(1 + var / mean2)))
)
def Q(nu, lambda_, x, epsilon=1e-5):
'''
This function is translated from a Matlab function originally written by S.M. Kay, see [1].
Q computes the right-tail probability of a central or noncentral chi-squared PDF.
Input Parameters:
nu = Degrees of Freedom (DoF)
lambda_ = Noncentrality parameter (0 for central chi-square)
x = Random variable
epsilon = maximum allowable error (should be a small number such as 1e-5) due to the truncation of the infinite sum
[1] S. Kay, Fundamental of statistical signal processing, Vol. 2: detection theory, Prentice-Hall, Upper Saddle River, NJ, 1998.
'''
from math import erfc, exp, factorial, pi, sqrt
normRT = lambda x: 0.5*erfc(x/sqrt(2))
t = exp(lambda_ / 2.0) * (1 - epsilon)
sum_ = 1
M = 0
while sum_ < t:
M += 1
sum_ += ((lambda_ / 2.0)**M) / factorial(M)
if nu / 2 - nu // 2: # nu is odd
P = 2 * normRT(sqrt(x))
g = Q2p = sqrt(2*x/pi) * exp(-x/2)
if nu > 1:
for m in range(5, nu+1, 2):
g *= x / (m-2)
Q2p += g
P += exp(-lambda_ / 2) * Q2p
for k in range(1, M+1):
m = nu + 2 * k
g *= x / (m - 2)
Q2p += g
arg = (exp(-lambda_/2) * (lambda_/2)**k) / factorial(k)
P += arg * Q2p
else: # nu == 1
P += exp(-lambda_ / 2) * (lambda_ / 2) * Q2p
for k in range(2, M+1):
m = nu + 2*k
g *= x / (m-2)
Q2p += g
arg = (exp(-lambda_ / 2) * (lambda_/2)**k) / factorial(k)
P += arg * Q2p
else: # nu is even
g = Q2 = exp(-x/2)
for m in range(4, nu+1, 2):
g *= x / (m-2)
Q2 += g
P = exp(-lambda_/2) * Q2
for k in range(1, M+1):
m = nu + 2*k
g *= x / (m-2)
Q2 += g
arg = (exp(-lambda_/2) * (lambda_/2)**k) / factorial(k)
P += arg * Q2
return P
def lognorm_cdf(x, mu, sigma):
"check wikipedia"
#print 'x:', x
if x == 0:
return 0
top = -(math.log(x)-mu)
down = sigma*math.sqrt(2)
return math.erfc(top/down)/2
def logncdf(x, mu, sigma): # 対数正規累積確率分布関数
if x < 0:
cdf = 0.0
elif sp.isposinf(x):
cdf = 1.0
else:
z = (sp.log(x) - mu) / float(sigma)
cdf = 0.5 * (math.erfc(-z / sp.sqrt(2)))
return cdf
def analytical_tr(T0, T1, kappa, t, z):
z = np.array(z) # to make sure it's an array
T = np.zeros(z.size)
for iz in range(z.size):
T[iz] = math.erfc(z[iz] / (2.0 * (kappa * t)**0.5)) * (T0 - T1) + T1
return T
def _CrosshairShotResults_getShotResult(base,
cls,
hitPoint,
collision,
direction,
excludeTeam=0,
piercingMultiplier=1):
if config.get('sight/enabled', True) and battle.isBattleTypeSupported:
global piercingActual, armorActual, shotResult, hitAngle, normHitAngle, piercingChance
old_piercingActual = piercingActual
old_armorActual = armorActual
old_hitAngle = hitAngle
piercingActual = None
armorActual = None
piercingChance = None
hitAngle = None
normHitAngle = None
shotResult = PIERCING_CHANCE_KEY[_SHOT_RESULT.UNDEFINED]
if collision is None:
if (old_armorActual != armorActual) or (
old_piercingActual != piercingActual) or (old_hitAngle !=
hitAngle):
as_event('ON_CALC_ARMOR')
return _SHOT_RESULT.UNDEFINED
entity = collision.entity
if entity.__class__.__name__ not in ('Vehicle', 'DestructibleEntity'):
if (old_armorActual != armorActual) or (
old_piercingActual != piercingActual) or (old_hitAngle !=
hitAngle):
as_event('ON_CALC_ARMOR')
return _SHOT_RESULT.UNDEFINED
if entity.health <= 0 or entity.publicInfo['team'] == excludeTeam:
if (old_armorActual != armorActual) or (
old_piercingActual != piercingActual) or (old_hitAngle !=
hitAngle):
as_event('ON_CALC_ARMOR')
return _SHOT_RESULT.UNDEFINED
player = BigWorld.player()
if player is None:
if (old_armorActual != armorActual) or (
old_piercingActual != piercingActual) or (old_hitAngle !=
hitAngle):
as_event('ON_CALC_ARMOR')
return _SHOT_RESULT.UNDEFINED
vDesc = player.getVehicleDescriptor()
shell = vDesc.shot.shell
caliber = shell.caliber
shellKind = shell.kind
ppDesc = vDesc.shot.piercingPower
maxDist = vDesc.shot.maxDistance
dist = (hitPoint - player.getOwnVehiclePosition()).length
piercingPower = cls._computePiercingPowerAtDist(
ppDesc, dist, maxDist, piercingMultiplier)
fullPiercingPower = piercingPower
minPP, maxPP = cls._computePiercingPowerRandomization(shell)
result = _SHOT_RESULT.NOT_PIERCED
isJet = False
jetStartDist = None
ignoredMaterials = set()
collisionsDetails = cls._getAllCollisionDetails(
hitPoint, direction, entity)
if collisionsDetails is None:
if (old_armorActual != armorActual) or (
old_piercingActual != piercingActual) or (old_hitAngle !=
hitAngle):
as_event('ON_CALC_ARMOR')
return _SHOT_RESULT.UNDEFINED
for cDetails in collisionsDetails:
if isJet:
jetDist = cDetails.dist - jetStartDist
if jetDist > 0.0:
piercingPower *= 1.0 - jetDist * cls._SHELL_EXTRA_DATA[
shellKind].jetLossPPByDist
if cDetails.matInfo is None:
result = cls._CRIT_ONLY_SHOT_RESULT
else:
matInfo = cDetails.matInfo
if (cDetails.compName, matInfo.kind) in ignoredMaterials:
continue
hitAngleCos = cDetails.hitAngleCos if matInfo.useHitAngle else 1.0
hitAngle = hitAngleCos
normHitAngle = hitAngle
if not isJet and cls._shouldRicochet(shellKind, hitAngleCos,
matInfo, caliber):
normHitAngle = -1.0
break
piercingPercent = 1000.0
if piercingPower > 0.0:
penetrationArmor = cls._computePenetrationArmor(
shellKind, hitAngleCos, matInfo, caliber)
normHitAngle = matInfo.armor / penetrationArmor if penetrationArmor != 0.0 else hitAngle
piercingPercent = 100.0 + (penetrationArmor - piercingPower
) / fullPiercingPower * 100.0
piercingActual = int(piercingPower)
armorActual = int(penetrationArmor)
# piercingChance = max(0, min(1.0, (piercingPower / penetrationArmor - 0.75) * 2)) if penetrationArmor > 0.0 else 1.0
armorRatio = penetrationArmor / piercingPower - 1.0
# piercingChance = 1.0 if armorRatio < -0.25 else 0.5 * math.erfc(8.485281374238576 * armorRatio) if armorRatio <= 0.25 else 0.0
if armorRatio < -0.25:
piercingChance = 1.0
elif armorRatio > 0.25:
piercingChance = 0.0
else:
piercingChance = 0.5 * math.erfc(
8.485281374238576 * armorRatio)
piercingPower -= penetrationArmor
# log('penetrationArmor = %s piercingPercent = %s piercingPower = %s' % (penetrationArmor, piercingPercent, piercingPower))
if matInfo.vehicleDamageFactor:
if minPP < piercingPercent < maxPP:
result = _SHOT_RESULT.LITTLE_PIERCED
elif piercingPercent <= minPP:
result = _SHOT_RESULT.GREAT_PIERCED
break
elif matInfo.extra:
if piercingPercent <= maxPP:
result = cls._CRIT_ONLY_SHOT_RESULT
if matInfo.collideOnceOnly:
ignoredMaterials.add((cDetails.compName, matInfo.kind))
if piercingPower <= 0.0:
break
if cls._SHELL_EXTRA_DATA[shellKind].jetLossPPByDist > 0.0:
isJet = True
mInfo = cDetails.matInfo
armor = mInfo.armor if mInfo is not None else 0.0
jetStartDist = cDetails.dist + armor * 0.001
shotResult = PIERCING_CHANCE_KEY[result]
if (old_armorActual !=
armorActual) or (old_piercingActual !=
piercingActual) or (old_hitAngle != hitAngle):
as_event('ON_CALC_ARMOR')
return result
else:
return base(hitPoint, collision, direction, excludeTeam)
import numpy as np
from astropy.io import fits
from scipy.stats.distributions import chi2
from astropy.cosmology import FlatLambdaCDM
import math
cosmo = FlatLambdaCDM(H0=70,Om0=.3)
filename = 'output_cats/mass_select.fits'
with fits.open(filename) as hdu:
data = hdu[1].data
mask = data['stellar_mass_50'] > 10
data = data[mask]
mask = data['redshift_50'] > 2
data = data[mask]
mask = (chi2.sf(data['chisq_phot'],(data['n_bands']-10))) > (0.5*math.erfc(5*(2**-0.5)))
data = data[mask]
age = cosmo.age(data['redshift_50']).value*(10**9)
factor = 0.2/age
mask = 10**data['sSFR_50'] < factor
data = data[mask]
print(data.shape)
newhdu = fits.BinTableHDU(data=data)
newhdu.writeto('output_cats/sample.fits')
def kendalltau(x, y, use_ties=True, use_missing=True, method='auto'):
assert x.size == y.size, "Both variables should have the same number of observations."
n = x.size
if n < 2:
return np.nan, np.nan
rx = rankdata(x, use_missing)
ry = rankdata(y, use_missing)
valid = (rx > 0) * (ry > 0)
rx = rx[valid]
ry = ry[valid]
n = np.sum(valid)
idx = rx.argsort()
(rx, ry) = (rx[idx], ry[idx])
C, D = 0, 0
for i in range(len(ry)-1):
C += ((ry[i+1:] > ry[i]) * (rx[i+1:] > rx[i])).sum()
D += ((ry[i+1:] < ry[i]) * (rx[i+1:] > rx[i])).sum()
xties, corr_x = count_tied_groups(x)
yties, corr_y = count_tied_groups(y)
if use_ties:
denom = np.sqrt((n*(n-1)-corr_x)/2. * (n*(n-1)-corr_y)/2.)
else:
denom = n*(n-1)/2.
if denom == 0.:
return np.nan, np.nan
tau = (C-D) / denom
if method == 'exact' and (len(xties) > 0 or len(yties) > 0):
raise ValueError("Ties found, exact method cannot be used.")
if method == 'auto':
if (len(xties) == 0 and len(yties) == 0) and (n <= 33 or min(C, n*(n-1)/2.0-C) <= 1):
method = 'exact'
else:
method = 'asymptotic'
if len(xties) == 0 and len(yties) == 0 and method == 'exact':
# Exact p-value, see Maurice G. Kendall, "Rank Correlation Methods" (4th Edition), Charles Griffin & Co., 1970.
c = int(min(C, (n*(n-1))/2-C))
if n <= 0:
raise ValueError
elif c < 0 or 2*c > n*(n-1):
raise ValueError
elif n == 1:
prob = 1.0
elif n == 2:
prob = 1.0
elif c == 0:
prob = 2.0/factorial(n)
elif c == 1:
prob = 2.0/factorial(n-1)
else:
old = [0.0]*(c+1)
new = [0.0]*(c+1)
new[0] = 1.0
new[1] = 1.0
for j in range(3,n+1):
old = new[:]
for k in range(1,min(j,c+1)):
new[k] += new[k-1]
for k in range(j,c+1):
new[k] += new[k-1] - old[k-j]
prob = 2.0*np.sum(np.asarray(new))/factorial(n)
elif method == 'asymptotic':
var_s = n*(n-1)*(2*n+5)
if use_ties:
v1x, v1y, v2x, v2y = 0, 0, 0, 0
for k, v in xties.items():
var_s -= v*k*(k-1)*(2*k+5)*1.
v1x += v*k*(k-1)
if n > 2:
v2x += v*k*(k-1)*(k-2)
for k, v in yties.items():
var_s -= v*k*(k-1)*(2*k+5)*1.
v1y += v*k*(k-1)
if n > 2:
v2y += v*k*(k-1)*(k-2)
v1 = v1x * v1y
v2 = v2x * v2y
v1 /= 2.*n*(n-1)
if n > 2:
v2 /= 9.*n*(n-1)*(n-2)
else:
v2 = 0
else:
v1 = v2 = 0
var_s /= 18.
var_s += (v1 + v2)
z = (C-D)/np.sqrt(var_s)
prob = erfc(abs(z)/np.sqrt(2))
return tau, prob
def normal_cdf(x): return .5 * math.erfc(-x / math.sqrt(2))
def erfc(self):
import math
return AdvFloat(math.erfc(self))
def pidistf(x):
y = 0.9
e = 4 + erfc(x / 5.3)
s = y * e
return s
def ber_mqam(EbN0, M):
k = math.log(M, 2)
return 2 / k * (1 - 1 / math.sqrt(M)) * math.erfc(
math.sqrt(3 * EbN0 * k / (2 * (M - 1))))
def madelung(screening_length=inf, g_ewald=7.1, kmax=12, approx=False):
"""Madelung constant for 1x1x1 Yukawa lattice with neutralizing background.
Keyword arguments:
screening_length -- the screening length (default inf)
g_ewald -- Ewald splitting parameter (default 7.1)
kmax -- range of reciprocal space sum (default 12)
approx -- whether to use closed-form approximation (default False)
See eqn (2.19) of Salin and Caillol, J. Chem. Phys. 113, 10459 (2000).
(alpha = 1/screening_length, beta = g_ewald)
"""
if isinf(screening_length):
return -2.837297479
if screening_length == 0:
return 0
a = 1.0 / screening_length # screening wavenumber
a2 = a * a
# closed-form approximation
if approx:
r = 0.911544
r2 = r * r
return (4 * pi / a2 *
(a * r + 1 + a2 * r2 / 3) - 1 / r) * exp(-a * r) - 4 * pi / a2
b = 2 * g_ewald
b2 = b * b
kmax2 = kmax * kmax
pi2 = pi * pi
s = 0 # running total
# Sum over the (+,+,+) octant, then multiply the result by 8.
for k in list(product(range(kmax + 1), repeat=3))[1:]:
k2 = k[0] * k[0] + k[1] * k[1] + k[2] * k[2]
if k2 <= kmax2:
q2 = 4 * pi2 * k2 # squared wavenumber
t = exp(-(q2 + a2) / b2) / (q2 + a2)
for i in range(3):
# Correct for overcounting when k is on an axial plane.
if k[i] == 0:
t /= 2
s += t
# This is where we multiply by 8.
# (We also need a 4*pi because we are using Gaussian units.)
s *= 32 * pi
# See last line of eqn (2.19) of Salin and Caillol.
# (Note the sign error in the final term.)
s -= b * exp(-a2 / b2) / sqrt(pi)
s += a * erfc(a / b)
if a > 0.001:
s += 4 * pi * (exp(-a2 / b2) - 1) / a2
else: # If a is small, use expansion about a = 0.
s += -4 * pi / b2 + 2 * pi * a2 / (b2 * b2) - 2 * pi * a2 * a2 / (
3 * b2 * b2 * b2)
return s
def main():
a = 5.873
b = 4
c = -2.7
# number-theoretic and representation functions
# https://docs.python.org/2/library/math.html#number-theoretic-and-representation-functions
print("\nNumber-theoretic and representation functions")
y = math.ceil(a)
print("math.ceil({}) = {}".format(a, y))
y = math.floor(a)
print("math.floor({}) = {}".format(a, y))
y = math.copysign(a, c)
print("math.copysign({}, {}) = {}".format(a, c, y))
y = math.fabs(c)
print("math.fabs({}) = {}".format(c, y))
y = math.factorial(b)
print("math.factorial({}) = {}".format(b, y))
y = math.fmod(a, b)
print("math.fmod({}, {}) = {}".format(a, b, y))
(y, z) = math.frexp(c)
print("math.frexp({}) = ({}, {})".format(c, y, z))
y = math.fsum([.1,.2,.3,.4,.5,.6,.7,.8,.9])
print("math.fsum([.1,.2,.3,.4,.5,.6,.7,.8,.9]) = {}".format(y))
y = math.isfinite(a)
print("math.isfinite({}) = {}".format(a, y))
y = math.isinf(a)
print("math.isinf({}) = {}".format(a, y))
y = math.isnan(c)
print("math.isnan({}) = {}".format(c, y))
y = math.ldexp(c, b)
print("math.ldexp({}, {}) = {}".format(c, b, y))
y = math.modf(a)
print("math.modf({}) = {}".format(a, y))
y = math.trunc(a)
print("math.trunc({}) = {}".format(a, y))
# Power and logarithmic functions
print("\nPower and logarithmic functions")
y = math.exp(b)
print("math.exp({}) = {}".format(b, y))
y = math.expm1(b)
print("math.expm1({}) = {}".format(b, y))
y = math.log(a)
print("math.log({}) = {}".format(a, y))
y = math.log1p(a)
print("math.log1p({}) = {}".format(a, y))
y = math.log2(a)
print("math.log2({}) = {}".format(a, y))
y = math.log10(a)
print("math.log10({}) = {}".format(a, y))
y = math.pow(a, b)
print("math.pow({}, {}) = {}".format(a, b, y))
y = math.sqrt(b)
print("math.sqrt({}) = {}".format(b, y))
# Trigonometric functions
print("\nTriginometric functions")
a = 0.24235
b = 0.5953
y = math.acos(a)
print("math.acos({}) = {}".format(a, y))
y = math.asin(a)
print("math.asin({}) = {}".format(a, y))
y = math.atan(a)
print("math.atan({}) = {}".format(a, y))
y = math.atan2(a,b)
print("math.atan2({},{}) = {}".format(a, b, y))
a = 90
b = 15
y = math.sin(a)
print("math.sin({}) = {}".format(a, y))
y = math.cos(a)
print("math.cos({}) = {}".format(a, y))
y = math.tan(a)
print("math.tan({}) = {}".format(a, y))
y = math.hypot(a, b)
print("math.hypot({}, {}) = {}".format(a, b, y))
# Angular conversion
print("\nAngular conversion")
a = 0.83
y = math.degrees(a)
print("math.degrees({}) = {}".format(a, y))
y = math.radians(b)
print("math.radians({}) = {}".format(b, y))
# Hyperbolic functions
print("\nHyperbolic functions")
a = 90
y = math.acosh(b)
print("math.acosh({}) = {}".format(b, y))
y = math.asinh(a)
print("math.asinh({}) = {}".format(a, y))
y = math.atanh(0.53)
print("math.atanh({}) = {}".format(0.53, y))
y = math.cosh(b)
print("math.cosh({}) = {}".format(b, y))
y = math.sinh(a)
print("math.sinh({}) = {}".format(a, y))
y = math.tanh(b)
print("math.tanh({}) = {}".format(b, y))
# Special functions
print("\nSpecial functions")
a = 34
y = math.erf(a)
print("math.erf({}) = {}".format(a, y))
y = math.erfc(a)
print("math.erfc({}) = {}".format(a, y))
y = math.gamma(a)
print("math.gamma({}) = {}".format(a, y))
y = math.lgamma(a)
print("math.lgamma({}) = {}".format(a, y))
math.sin(x) # Return the sine of x radians. math.tan(x) # Return the tangent of x radians. math.degrees(x) # Converts angle x from radians to degrees. math.radians(x) # Converts angle x from degrees to radians. ################# Hyperbolic functions ################# math.acosh(x) # Return the inverse hyperbolic cosine of x. math.asinh(x) # Return the inverse hyperbolic sine of x. math.atanh(x) # Return the inverse hyperbolic tangent of x. math.cosh(x) # Return the hyperbolic cosine of x. math.sinh(x) # Return the hyperbolic sine of x. math.tanh(x) # Return the hyperbolic tangent of x. ################# Special functions ################# math.erf(x) # Return the error function at x. math.erfc(x) # Return the complementary error function at x. math.gamma(x) # Return the Gamma function at x. math.lgamma(x) # Return the natural logarithm of the absolute value of the Gamma function at x. ################# Constants ################# math.pi # The mathematical constant π = 3.141592..., to available precision. math.e # The mathematical constant e = 2.718281..., to available precision. # Example import math import time
def main():
with open(sys.argv[1], 'r') as f:
sample = f.readline()
table = {}
bin_sample = hex2bin(sample)
n = len(bin_sample)
# Calculate best values for L and Q based on length_bin_sample
# [n, L, Q = 2 * 10^L, expectedValue, variance]
input_size = [
[387840, 6, 640, 5.2177052, 2.954],
[904960, 7, 1280, 6.1962507, 3.125],
[2068480, 8, 2560, 7.1836656, 3.238],
[4654080, 9, 5120, 8.1764248, 3.311],
[10342400, 10, 10240, 9.1723243, 3.35],
[22753280, 11, 20480, 10.170032, 3.384],
[49643520, 12, 40960, 11.168765, 3.401],
[107560960, 13, 81920, 12.168070, 3.410],
[231669760, 14, 163840, 13.167693, 3.416],
[496435200, 15, 327680, 14.167488, 3.419],
[1059061760, 16, 655360, 15.167379, 3.421]
]
L = input_size[0][1]
Q = input_size[0][2]
expectedValue = input_size[0][3]
variance = input_size[0][4]
for i in range(1, len(input_size) - 1):
if (input_size[i][0] >= n) and (input_size[i + 1][0] < n):
L = input_size[i][1]
Q = input_size[i][2]
expectedValue = input_size[i][3]
variance = input_size[i][4]
break
if n >= input_size[len(input_size) - 1][0]:
L = input_size[len(input_size) - 1][1]
Q = input_size[len(input_size) - 1][2]
expectedValue = input_size[len(input_size) - 1][3]
variance = input_size[len(input_size) - 1][4]
initialization_segment = bin_sample[0 : Q * L]
K = n/L - Q
test_segment = bin_sample[Q * L : (Q + K) * L]
backtrack("", L, table)
for i in range((Q - 1) * L, -1, -L):
block_id = i/L + 1
block = str(initialization_segment[i : i + L])
if table[block] < block_id:
table[block] = block_id
sum = 0
for i in range(0, K * L, L):
block_id = Q + i/L + 1
block = str(test_segment[i : i + L])
diff = block_id - table[block]
sum += math.log(diff, 2)
table[block] = block_id
fn = sum / K
c = 0.7 - 0.8/L + (4 + 32/L) * math.pow(K, -3/L) / 15
sigma = c * math.sqrt(variance/K)
pvalue = math.erfc(math.fabs((fn - expectedValue) / (math.sqrt(2) * sigma)))
print 'P-value: ' + str(pvalue)
if (pvalue < 0.1):
print 'Sequence is non-random'
else:
print 'Sequence is random'
def FitEMG(x, a, b, c):
y = (a / 2) * math.exp((a / 2) * (2 * b + a * c**2 - 2 * x)) * math.erfc(
(b + a * c * +2 - x) / (math.sqrt(2) * c))
return y
def math_erfc(A, B):
i = cuda.grid(1)
B[i] = math.erfc(A[i])
def neon_math_erfc(self):
x = self.stack.pop().value
self.stack.append(Value(decimal.Decimal(math.erfc(float(x)))))
def maurers_universal_test(bits, patternlen=None, initblocks=None):
n = len(bits)
# Step 1. Choose the block size
if patternlen != None:
L = patternlen
else:
ns = [904960, 2068480, 4654080, 10342400,
22753280, 49643520, 107560960,
231669760, 496435200, 1059061760]
L = 6
if n < 387840:
print("Error. Need at least 387840 bits. Got %d." % n)
# exit()
return False, 0.0, None
for threshold in ns:
if n >= threshold:
L += 1
# Step 2 Split the data into Q and K blocks
nblocks = int(math.floor(n / L))
if initblocks != None:
Q = initblocks
else:
Q = 10 * (2 ** L)
K = nblocks - Q
# Step 3 Construct Table
nsymbols = (2 ** L)
T = [0 for x in range(nsymbols)] # zero out the table
for i in range(Q): # Mark final position of
pattern = bits[i * L:(i + 1) * L] # each pattern
idx = pattern2int(pattern)
T[idx] = i + 1 # +1 to number indexes 1..(2**L)+1
# instead of 0..2**L
# Step 4 Iterate
sum = 0.0
for i in range(Q, nblocks):
pattern = bits[i * L:(i + 1) * L]
j = pattern2int(pattern)
dist = i + 1 - T[j]
T[j] = i + 1
sum = sum + math.log(dist, 2)
print(" sum =", sum)
# Step 5 Compute the test statistic
fn = sum / K
print(" fn =", fn)
# Step 6 Compute the P Value
# Tables from https://static.aminer.org/pdf/PDF/000/120/333/
# a_universal_statistical_test_for_random_bit_generators.pdf
ev_table = [0, 0.73264948, 1.5374383, 2.40160681, 3.31122472,
4.25342659, 5.2177052, 6.1962507, 7.1836656,
8.1764248, 9.1723243, 10.170032, 11.168765,
12.168070, 13.167693, 14.167488, 15.167379]
var_table = [0, 0.690, 1.338, 1.901, 2.358, 2.705, 2.954, 3.125,
3.238, 3.311, 3.356, 3.384, 3.401, 3.410, 3.416,
3.419, 3.421]
# sigma = math.sqrt(var_table[L])
mag = abs((fn - ev_table[L]) / (
(0.7 - 0.8 / L + (4 + 32 / L) * (pow(K, -3 / L)) / 15) * (math.sqrt(var_table[L] / K)) * math.sqrt(2)))
P = math.erfc(mag)
success = (P >= 0.01)
return (success, P, None)
def normal_cdf(x, mu, sig):
return erfc((mu - x) / sig / SQRT2) / 2.0
alc_indices = range(2)
excls = {0: (), 1: ()}
atmtypes = [('DUM_HC', 'DUM_HC'), ('DUM_OW_spc', 'DUM_OW_spc')]
charges = {0: (0.1, 0.0), 1: (-0.1, 0.0)}
rtol = 1e-6
rc = 0.9
# determine ewald stuff
xvals = np.linspace(0, 5, 1000000)
vals = np.zeros_like(xvals)
for i, x in enumerate(xvals):
vals[i] = erfc(x)
etol_ind = np.argmax(vals < rtol)
beta_smooth = xvals[etol_ind] / rc
print("smoothing width: {}".format(beta_smooth))
ke = 138.9354859 # conv factor to get kJ/mol
fudge = 1.0
ewald_self_this = 0.0
ewald_self_for = [0.0 for for_lmbda in for_lmbdas]
for alc_idx in alc_indices:
charge_a, charge_b = charges[alc_idx]
ewald_self_this += -ke * beta_smooth / np.sqrt(np.pi) * (
def qfunc(x):
y = 0.5 * math.erfc(np.sqrt(x / 2))
return y
def test(input, n, patternlen=None, initblocks=None):
# Step 1. Choose the block size
if patternlen != None:
L = patternlen
else:
ns = [904960,2068480,4654080,10342400,
22753280,49643520,107560960,
231669760,496435200,1059061760]
L = 6
if n < 387840:
# Too little data. Inputs of length at least 387840 are recommended
return [0] * 8
for threshold in ns:
if n >= threshold:
L += 1
# Step 2 Split the data into Q and K blocks
nblocks = int(math.floor(n/L))
if initblocks != None:
Q = initblocks
else:
Q = 10*(2**L)
K = nblocks - Q
# Step 3 Construct Table
nsymbols = (2**L)
T=[0 for x in range(nsymbols)] # zero out the table
for i in range(Q): # Mark final position of
pattern = input[i*L:(i+1)*L] # each pattern
idx = int(pattern, 2)
T[idx]=i+1 # +1 to number indexes 1..(2**L)+1
# instead of 0..2**L
# Step 4 Iterate
sum = 0.0
for i in range(Q,nblocks):
pattern = input[i*L:(i+1)*L]
j = int(pattern,2)
dist = i+1-T[j]
T[j] = i+1
sum = sum + math.log(dist,2)
# Step 5 Compute the test statistic
fn = sum/K
# Step 6 Compute the P Value
# Tables from https://static.aminer.org/pdf/PDF/000/120/333/
# a_universal_statistical_test_for_random_bit_generators.pdf
ev_table = [0,0.73264948,1.5374383,2.40160681,3.31122472,
4.25342659,5.2177052,6.1962507,7.1836656,
8.1764248,9.1723243,10.170032,11.168765,
12.168070,13.167693,14.167488,15.167379]
var_table = [0,0.690,1.338,1.901,2.358,2.705,2.954,3.125,
3.238,3.311,3.356,3.384,3.401,3.410,3.416,
3.419,3.421]
# sigma = math.sqrt(var_table[L])
sigma = abs((fn - ev_table[L])/((math.sqrt(var_table[L]))*math.sqrt(2)))
P = math.erfc(sigma)
success = (P >= 0.01)
return [n, nblocks, L, K, Q, sigma, P, success]
os.system('clear')
loop = 0
Pe = [0,0,0,0,0,0,0,0,0,0,0,0,0]
ber_sim = [0,0,0,0,0,0,0,0,0,0,0,0,0]
SNRdb = [-2,-1,0,1,2,3,4,5,6,7,8,9,10]
No_of_bits = 100000000 # 1e8
for iter in range(1,14,1):
#for SNRdb in range(-2,2,1):
SNR = 10**(SNRdb[loop]/10.0) # linear SNR
Pe[loop] = 0.5*erfc(np.sqrt(SNR))
#print(Pe[loop])
No = 1/SNR
#print(No)
tx_sig = np.random.binomial(n=1, p=0.5, size=No_of_bits)
tx_sig = 2*tx_sig-1
#print(tx_sig)
noise = np.sqrt(No/2)*np.random.randn(No_of_bits)
#print(noise)
rx_sig = tx_sig + noise
#rx_sig = conv(tx_sig, multi_path_channel) + noise
#print(rx_sig)
decision = np.sign(rx_sig)
#print(decision)
err = decision - tx_sig
def erfc(x):
return math.erfc(x)
print
print '{:^3} {:^6} {:^6} {:^6}'.format('R', 'Arcsin', 'Arccos', 'Arctan')
print '{:-^3} {:-^6} {:-^6} {:-^6}'.format('', '', '', '')
for r in [ 0, 0.5, 1 ]:
print '{:3.1f} {:6.4f} {:6.4f} {:6.4f}'.format( r, math.asin(r), math.acos(r), math.atan(r) )
print
## 5.4.10 Hyperbolic Functions
# Hyperbolic functions appear in linear differential equations
print '{:^4} {:^6} {:^6} {:^6}'.format('X', 'sinh', 'cosh', 'tanh')
print '{:-^4} {:-^6} {:-^6} {:-^6}'.format('', '', '', '')
for x in xrange(0, 11, 2):
x = x/10.0
print '{:4.2f} {:6.4f} {:6.4f} {:6.4f}'.format( x, math.sinh(x), math.cosh(x), math.tanh(x) )
print
## 5.4.11 Special Functions
# Gauss Error function [ erf(-x) == -erf(x)
print '{:^5} {:7}'.format('X', 'erf(x)')
print '{:-^5} {:-^7}'.format('', '')
for x in [-3, -2, -1, -0.5, -0.25, 0, 0.25, 0.5, 1, 2, 3]:
print '{:5.2f} {:7.4f}'.format( x, math.erf(x) )
print
# And the complimentary error functions
print '{:^5} {:7}'.format('X', 'erfc(x)')
print '{:-^5} {:-^7}'.format('', '')
for x in [-3, -2, -1, -0.5, -0.25, 0, 0.25, 0.5, 1, 2, 3]:
print '{:5.2f} {:7.4f}'.format( x, math.erfc(x) )
print
def Q(x):
return (1 / 2) * math.erfc(x / math.sqrt(2))
def normcdf(n):
return 0.5 * math.erfc(-n * math.sqrt(0.5))
def pvalue(x, sigma):
return 0.5 * erfc(x / (sigma * np.sqrt(2)))
import matplotlib.pyplot as plt
import numpy as np
import math as mt
B = np.linspace(0, 20, 200)
A = [2, 4, 8, 16, 32, 64]
C = np.ones([200]) * 0.02
print(C)
for i in range(6):
M = A[i]
y = [(mt.sqrt(M) - 1)/mt.sqrt(M)*mt.log(M,2) * mt.erfc(mt.sqrt(3*mt.log(M,2)*(10**(x/10))/(2*M-2))) + \
(mt.sqrt(M) - 2) / mt.sqrt(M) * mt.log(M, 2) * mt.erfc(mt.sqrt(3 * mt.log(M, 2)*(10**(x/10)) / (2 * M - 2))) for x in B]
plt.plot(B, y, '.')
plt.plot(B, C, '-')
plt.semilogy(B, y)
plt.ylim(0.0, 100)
plt.show()
def ber_qpsk(EbN0):
return 0.5 * math.erfc(math.sqrt(EbN0))
# Hyperbolic functions
#
if not math.isclose(math.sinh(1), (math.e - 1 / math.e) / 2):
fail("math.isclose(math.sinh(1), (math.e - 1/math.e) / 2)")
if not math.isclose(math.cosh(1), (math.e + 1 / math.e) / 2):
fail("math.isclose(math.cosh(1), (math.e + 1/math.e) / 2)")
if not math.isclose(math.tanh(1), math.sinh(1) / math.cosh(1)):
fail("math.isclose(math.tanh(1), math.sinh(1)/math.cosh(1))")
if not math.isclose(math.asinh(math.sinh(1)), 1):
fail("math.isclose(math.asinh(math.sinh(1)), 1)")
if not math.isclose(math.acosh(math.cosh(1)), 1):
fail("math.isclose(math.acosh(math.cosh(1)), 1)")
if not math.isclose(math.atanh(math.tanh(1)), 1):
fail("math.isclose(math.atanh(math.tanh(1)), 1)")
#
# Special functions
#
if not math.isclose(math.erf(1), 0.8427007929497149):
fail("math.isclose(math.erf(1), 0.8427007929497149)")
if not math.isclose(math.erfc(1), 1 - math.erf(1)):
fail("math.isclose(math.erfc(1), 1-math.erf(1))")
if not math.isclose(math.gamma(10), math.factorial(9)):
fail("math.isclose(math.gamma(10), math.factorial(9))")
if not math.isclose(math.lgamma(10), math.log(math.factorial(9))):
fail("math.isclose(math.lgamma(10), math.log(math.factorial(9)))")
#
# Constants
#
if not math.isclose(math.pi * 2, math.tau):
fail("math.isclose(math.pi * 2, math.tau)")
def _slow_ndtr_cpu(x):
return 0.5 * math.erfc(-x / 2**0.5)
def ber_mpsk(EbN0, M):
k = math.log(M, 2)
return 1 / k * math.erfc(math.sqrt(EbN0 * k) * math.sin(math.pi / M))
