def findNthPolygonalNumber( n, k ):
if real_int( k ) < 3:
raise ValueError( 'the number of sides of the polygon cannot be less than 3,' )
return nint( fdiv( fsum( [ sqrt( fsum( [ power( k, 2 ), fprod( [ 8, k, real( n ) ] ),
fneg( fmul( 8, k ) ), fneg( fmul( 16, n ) ), 16 ] ) ),
k, -4 ] ), fmul( 2, fsub( k, 2 ) ) ) )
def calculateAntiharmonicMean( args ):
if isinstance( args, RPNGenerator ):
return calculateAntiharmonicMean( list( args ) )
elif isinstance( args, list ):
if isinstance( args[ 0 ], ( list, RPNGenerator ) ):
return [ calculateAntiharmonicMean( list( arg ) ) for arg in args ]
else:
return fdiv( fsum( args, squared=True ), fsum( args ) )
else:
return args
def getStandardDeviation( args ):
if isinstance( args, RPNGenerator ):
return getStandardDeviation( list( args ) )
elif isinstance( args[ 0 ], ( list, RPNGenerator ) ):
return [ getStandardDeviation( arg ) for arg in args ]
mean = fsum( args ) / len( args )
dev = [ power( fsub( i, mean ), 2 ) for i in args ]
return sqrt( fsum( dev ) / len( dev ) )
def test_gth_solve_randmatrix():
N = 5
for j in range(10):
A = mp.randmatrix(N, N)
for i in range(N):
A[i, :] /= mp.fsum(A[i, :])
A[i, i] = -mp.fsum((A[i, j] for j in range(N) if j != i))
run_gth_solve(A, verbose=VERBOSE)
def step(array):
global _INFILE
global _BETA
global _NSTEP
beta = _BETA
old_positions, Ntides, is_3prime = array
internal = Aptamer("leaprc.ff12SB",_INFILE)
identifier = Ntides.replace(" ","")
internal.sequence(identifier,Ntides.strip())
internal.unify(identifier)
internal.command("saveamberparm union %s.prmtop %s.inpcrd"%(identifier,identifier))
time.sleep(2)
#print("WhereamI?")
print("Identifier: "+Ntides)
volume = (2*math.pi)**5
aptamer_top = app.AmberPrmtopFile("%s.prmtop"%identifier)
aptamer_crd = app.AmberInpcrdFile("%s.inpcrd"%identifier)
# print("loaded")
# if is_3prime == 1:
en_pos = [mcmc_sample(aptamer_top, aptamer_crd, old_positions, index, Nsteps=_NSTEP) for index in range(10)]
# else:
# en_pos_task = [mcmc_sample_five(aptamer_top, aptamer_crd, old_positions, index, Nsteps=200) for index in range(20)]
# barrier()
# en_pos = value(en_pos_task)
en = []
positions = []
positions_s = []
for elem in en_pos:
en += elem[0]
#print(elem[2], elem[1])
positions_s.append([elem[2], elem[1]])
positions = min(positions_s)[1]
fil = open("best_structure%s.pdb"%Ntides,"w")
app.PDBFile.writeModel(aptamer_top.topology,positions,file=fil)
fil.close()
del fil
Z = volume*math.fsum([math.exp(-beta*elem) for elem in en])/len(en)
P = [math.exp(-beta*elem)/Z for elem in en]
S = volume*math.fsum([-elem*math.log(elem*volume) for elem in P])/len(P)
print("%s : %s"%(Ntides,S))
return positions, Ntides, S
def getNthNonagonalSquareNumber( n ):
if real( n ) < 0:
ValueError( '' )
p = fsum( [ fmul( 8, sqrt( 7 ) ), fmul( 9, sqrt( 14 ) ), fmul( -7, sqrt( 2 ) ), -28 ] )
q = fsum( [ fmul( 7, sqrt( 2 ) ), fmul( 9, sqrt( 14 ) ), fmul( -8, sqrt( 7 ) ), -28 ] )
sign = power( -1, real_int( n ) )
index = fdiv( fsub( fmul( fadd( p, fmul( q, sign ) ),
power( fadd( fmul( 2, sqrt( 2 ) ), sqrt( 7 ) ), n ) ),
fmul( fsub( p, fmul( q, sign ) ),
power( fsub( fmul( 2, sqrt( 2 ) ), sqrt( 7 ) ), fsub( n, 1 ) ) ) ), 112 )
return nint( power( nint( index ), 2 ) )
def dpint(f,snr): '''Integrand of the detection probability of single sources. Since it contains a modified Bessel function, which gets very big values, it has to be defined in a special way.''' big=mpmath.log(mpmath.besseli(1,snr*np.sqrt(2.*f))) small=mpmath.mpf(-f-0.5*snr**2.) normal=mpmath.log(np.sqrt(2.*f)*1./snr) result=mpmath.exp(mpmath.fsum([big,small,normal])) return float(result) #In the end the result should be between 0 and some sizeable number, so a float should be enough.
def sf(self, z):
"""
Compute the survival function of the truncated distribution
Parameters
----------
z : float
Minimum bound of the interval
Returns
-------
sf : float
The survival function of the truncated distribution
sf(z) = P( X > z | X is in intervals )
"""
intervals = self.intervals
Q, sumQ = self._Q, self._sumQ
N = len(Q)
dps = self._dps
k, (a, b) = min( (k, (a, b)) for k, (a, b) in enumerate(intervals) if b > z)
sf = fsum(Q[k+1:]) + self._cdf_notTruncated(max(a, z), b, dps)
sf /= sumQ
return sf
def getNthKFibonacciNumber( n, k ):
if real( n ) < 0:
raise ValueError( 'non-negative argument expected' )
if real( k ) < 2:
raise ValueError( 'argument <= 2 expected' )
if n < k - 1:
return 0
nth = int( n ) + 4
precision = int( fdiv( fmul( n, k ), 8 ) )
if ( mp.dps < precision ):
mp.dps = precision
poly = [ 1 ]
poly.extend( [ -1 ] * int( k ) )
roots = polyroots( poly )
nthPoly = getNthFibonacciPolynomial( k )
result = 0
exponent = fsum( [ nth, fneg( k ), -2 ] )
for i in range( 0, int( k ) ):
result += fdiv( power( roots[ i ], exponent ), polyval( nthPoly, roots[ i ] ) )
return floor( fadd( re( result ), fdiv( 1, 2 ) ) )
def calculateWindChill( measurement1, measurement2 ):
validUnitTypes = [
[ 'velocity', 'temperature' ],
]
arguments = matchUnitTypes( [ measurement1, measurement2 ], validUnitTypes )
if not arguments:
raise ValueError( '\'wind_chill\' requires velocity and temperature measurements' )
wind_speed = arguments[ 'velocity' ].convert( 'miles/hour' ).value
temperature = arguments[ 'temperature' ].convert( 'degrees_F' ).value
if wind_speed < 3:
raise ValueError( '\'wind_chill\' is not defined for wind speeds less than 3 mph' )
if temperature > 50:
raise ValueError( '\'wind_chill\' is not defined for temperatures over 50 degrees fahrenheit' )
result = fsum( [ 35.74, fmul( temperature, 0.6215 ), fneg( fmul( 35.75, power( wind_speed, 0.16 ) ) ),
fprod( [ 0.4275, temperature, power( wind_speed, 0.16 ) ] ) ] )
# in case someone puts in a silly velocity
if result < -459.67:
result = -459.67
return RPNMeasurement( result, 'degrees_F' ).convert( arguments[ 'temperature' ].units )
def invFourier(x,F):
k1 = r2*mpm.pi
f = []
for xi in x:
kx = k1*(xi/Lx)
f.append( mpm.fsum( F[ki]*mpm.cos(kx*mpm.mpf(ki)) \
for ki in xrange(len(F)) ) )
return f
def findCenteredPolygonalNumber( n, k ):
if real_int( k ) < 3:
raise ValueError( 'the number of sides of the polygon cannot be less than 3,' )
s = fdiv( k, 2 )
return nint( fdiv( fadd( sqrt( s ),
sqrt( fsum( [ fmul( 4, real( n ) ), s, -4 ] ) ) ), fmul( 2, sqrt( s ) ) ) )
def getMultinomial( args ):
numerator = fac( fsum( args ) )
denominator = 1
for arg in args:
denominator = fmul( denominator, fac( arg ) )
return fdiv( numerator, denominator )
def within(self, distance):
if self._within is None:
# s_w is the sum of within-cluster (point to its medoid) distances.
m = self.medoid
s_w = fsum(distance(i, m) for i in self.members if i != m)
n_w = len(self.members)
self._within = (s_w, n_w)
return self._within
def steady_state_eig(_matrix):
values, vectors = eig(_matrix)
real_values = []
for num in values:
real_values.append(num.real)
largest_eig_values = two_largest(real_values) # want the largest numbers because they should all be negative
_index = real_values.index(max(real_values))
steady_state_raw = vectors[:, _index]
steady_state = steady_state_raw / fsum(steady_state_raw)
return steady_state, largest_eig_values
def getNthNonagonalTriangularNumber( n ):
a = fmul( 3, sqrt( 7 ) )
b = fadd( 8, a )
c = fsub( 8, a )
return nint( fsum( [ fdiv( 5, 14 ),
fmul( fdiv( 9, 28 ), fadd( power( b, real_int( n ) ), power( c, n ) ) ),
fprod( [ fdiv( 3, 28 ),
sqrt( 7 ),
fsub( power( b, n ), power( c, n ) ) ] ) ] ) )
def test_stoch_eig_randmatrix():
N = 5
for j in range(10):
P = mp.randmatrix(N, N)
for i in range(N):
P[i, :] /= mp.fsum(P[i, :])
run_stoch_eig(P, verbose=VERBOSE)
def calculateArithmeticMean( args ):
if isinstance( args, RPNGenerator ):
return calculateArithmeticMean( list( args ) )
elif isinstance( args, list ):
if isinstance( args[ 0 ], ( list, RPNGenerator ) ):
return [ calculateGeometricMean( list( arg ) ) for arg in args ]
else:
return fdiv( fsum( args ), len( args ) )
else:
return args
def Fourier(N,f):
k1 = r2*mpm.pi
x = [-r1/r2+mpm.mpf(i)/mpm.mpf(2*N) for i in xrange(2*N)]
fx = [f(Lx*xi) for xi in x]
F = []
for ki in xrange(N):
kx = k1*mpm.mpf(ki)
F.append( mpm.fsum( fi*mpm.cos(kx*xi) for xi,fi in zip(x,fx) ) )
F[-1] /= mpm.mpf(N)
F[0] /= r2 # scale the first coefficient (mean value)
return F
def _boxcox_llf_deriv_not_finished(lmb, x):
"""
This function assumes lmb != 0.
"""
lmb = mpmath.mpf(lmb)
x = [mpmath.mpf(t) for t in x]
n = len(x)
logdata = [mpmath.log(t) for t in x]
sumlogdata = mpmath.fsum(logdata)
mean_deriv_bc_sq = mpmath.fsum(2*(t**lmb/lmb)**2*(mpmath.log(t) - 1/lmb)
for t in x) / n
mean_bc_data = mpmath.fsum(t**lmb/lmb for t in x) / n
deriv_mean_bc_data = mpmath.fsum(t**lmb/lmb * (mpmath.log(t) - 1/lmb)
for t in x) / n
dvar = mean_deriv_bc_sq - 2 * mean_bc_data * deriv_mean_bc_data
return sumlogdata - n/2 * dvar
def sf(k, nc, ntotal, ngood, nsample):
"""
Survival function of Fisher's noncentral hypergeometric distribution.
"""
_hg._validate(ntotal, ngood, nsample)
sup, p = support(nc, ntotal, ngood, nsample)
if k < sup[0]:
return mpmath.mp.one
elif k >= sup[-1]:
return mpmath.mp.zero
else:
return mpmath.fsum(p[k - sup[0] + 1:])
def _cdf_term(k, x, dfn, dfd, nc):
halfnc = nc / 2
halfdfn = dfn / 2
halfdfd = dfd / 2
log_coeff = _mp.fsum([k * _mp.log(halfnc), -halfnc, -_mp.loggamma(k + 1)])
coeff = _mp.exp(log_coeff)
r = coeff * _mp.betainc(a=halfdfn + k,
b=halfdfd,
x1=0,
x2=dfn * x / (dfd + dfn * x),
regularized=True)
return r
def calculate_RAM_usage(shape):
"""
Calculate a lower bound to the RAM needed to allocate the arrays for efficient_gcf_calculation
8 arrays of shape full of 64-bit floats.
There are also some lists whose space is hard to estimate.
:param shape: see efficient_gcf_calculation
:param length: see efficient_gcf_calculation
:return float: RAM usage in bytes
"""
c = 200.
return 8. * mp.fprod(shape) * 8. + c * mp.fsum(shape) * 8.
def getNthDecagonalCenteredSquareNumber( n ):
sqrt10 = sqrt( 10 )
dps = 7 * int( real_int( n ) )
if mp.dps < dps:
mp.dps = dps
return nint( floor( fsum( [ fdiv( 1, 8 ),
fmul( fdiv( 7, 16 ), power( fsub( 721, fmul( 228, sqrt10 ) ), fsub( n, 1 ) ) ),
fmul( fmul( fdiv( 1, 8 ), power( fsub( 721, fmul( 228, sqrt10 ) ), fsub( n, 1 ) ) ), sqrt10 ),
fmul( fmul( fdiv( 1, 8 ), power( fadd( 721, fmul( 228, sqrt10 ) ), fsub( n, 1 ) ) ), sqrt10 ),
fmul( fdiv( 7, 16 ), power( fadd( 721, fmul( 228, sqrt10 ) ), fsub( n, 1 ) ) ) ] ) ) )
def multi_segment_score_pv(score, num_segments, raw=True):
"""
Compute p-value for normalized score when considering
multiple high scoring segments. This functions considers
the normalized score Sr', i.e., the normalized score
of the HSP at rank r. For r=1, this formula is equivalent
to single_segment_score_pv
Computes formula [3] in Karlin & Altschul, PNAS 1993
Prob(Sr' >= x) ~ 1 - exp(-exp(-x)) * SUM (k=0 ... r - 1) { exp(-kx) / k! }
Implementation detail:
Python's range is not right-inclusive,
go up to r, not r - 1 for summation
:param score:
:param num_segments:
:param raw: return raw P-value instead of -log10(pv)
:return:
"""
with mpm.workprec(NUM_PREC_KA_PV):
def create_summand(sum_x, k):
prec_k = mpm.convert(k)
enum = mpm.exp(mpm.fneg(mpm.fmul(prec_k, sum_x)))
denom = mpm.factorial(prec_k)
summand = mpm.fdiv(enum, denom)
return summand
x = mpm.convert(score)
r = num_segments
complement = mpm.convert('1')
factor1 = mpm.exp(mpm.fneg(mpm.exp(mpm.fneg(x))))
factor2 = mpm.fsum(map(lambda k: create_summand(x, k), range(0, r)))
res = mpm.fsub(complement, mpm.fmul(factor1, factor2))
if not raw:
res = mpm.fneg(mpm.log10(res))
res = float(res)
# Equivalent implementation using Python standard library:
#
# x = score
# r = num_segments
# factor_1 = math.exp(-math.exp(-x))
# factor_2 = math.fsum(map(lambda k: math.exp(-k * x) / math.factorial(k), range(0, r)))
# res = 1 - factor_1 * factor_2
# if not raw:
# res = -1 * math.log10(res)
return res
def normm(A, prec):
M, N = np.array(A, ndmin=2).shape
AN = np.array(A, ndmin=2)
rows = M
cols = N
vals = []
for i in range(rows):
for j in range(cols):
vi = mv(mp.fabs(AN[i][j]), prec)**mv(2, prec)
vals.append(vi)
vf = mv(mp.fsum(vals), prec)**mv((1 / 2), prec)
return vf
def logpmf(k, ntotal, ngood, untilnbad):
"""
Logarithm of the prob. mass function of the negative hypergeometric distr.
"""
_validate(ntotal, ngood, untilnbad)
if k < 0 or k > ngood:
return mpmath.mp.ninf
with mpmath.extradps(5):
t1 = logbinomial(k + untilnbad - 1, k)
t2 = logbinomial(ntotal - untilnbad - k, ngood - k)
t3 = logbinomial(ntotal, ngood)
return mpmath.fsum([t1, t2, -t3])
def isOrderKSmithNumber(n, k):
if isPrime(n) or n < 2:
return 0
digitList1 = getDigitList(n, dropZeroes=True)
digitList2 = [
item for sublist in
[getDigitList(m, dropZeroes=True) for m in getFactors(n)]
for item in sublist
]
if sorted(digitList1) == sorted(digitList2):
return 0
sum1 = fsum([power(i, k) for i in getDigitList(n)])
sum2 = fsum([
power(j, k) for j in [
item for sublist in [getDigitList(m) for m in getFactors(n)]
for item in sublist
]
])
return 1 if sum1 == sum2 else 0
def __init__(self, clusterer, k):
distance = clusterer._distance_lambda()
n = clusterer._n
self._n = n
self._k = k
self._distance = distance
self._reset_random_swap()
self._selected = _agoras(n, k, distance)
self._selected.sort()
self._clusters = [None] * n
self._cost = fsum(self._update_clusters(self._unselected))
self._debug = clusterer.debug
def __init__(self, intervals):
"""
Create a new truncated distribution object
This method is abstract : it has to be overriden
Parameters
----------
intervals : [(float, float)]
The intervals the distribution is truncated to
"""
self.intervals = intervals
dps = 15
not_precise = True
while not_precise:
dps *= 2.
Q = [self._cdf_notTruncated(a, b, dps) for a, b in intervals]
not_precise = (fsum(Q) == 0.)
self._sumQ = fsum(Q)
self._dps = dps
self._Q = Q
def gmean(x, weights=None):
"""
Geometric mean of the values in the sequence x.
All the values in x must be nonnegative.
If weights is not None, it must be a sequence with the same length
as x. The sum of weights must not be zero.
"""
if any(t < 0 for t in x):
raise ValueError("all values in x must be nonnegative.")
with mpmath.extraprec(16):
if weights is None:
if 0 in x:
return mpmath.mp.zero
return mpmath.exp(mean([mpmath.log(t) for t in x]))
else:
# Weighted geometric mean
wsum = mpmath.fsum(weights)
if wsum == 0:
raise ValueError('sum of weights must not be 0.')
wlogxsum = mpmath.fsum([_xlogy(wi, xi)
for (xi, wi) in zip(x, weights)])
return mpmath.exp(wlogxsum / wsum)
def __init__(self, clusterer, k):
distance = clusterer._distance_lambda()
n = clusterer._n
self._n = n
self._k = k
self._distance = distance
self._reset_random_swap()
self._selected = _agoras(n, k, distance)
self._selected.sort()
self._clusters = [None] * n
self._cost = fsum(self._update_clusters(self._unselected))
self._debug = clusterer.debug
def logbeta(x, y):
"""
Natural logarithm of beta(x, y).
The beta function is
Gamma(x) Gamma(y)
beta(x, y) = -----------------
Gamma(x + y)
where Gamma(z) is the Gamma function.
"""
with mpmath.extradps(5):
return (mpmath.loggamma(x) + mpmath.loggamma(y) -
mpmath.loggamma(mpmath.fsum([x, y])))
def __init__(self, intervals):
"""
Create a new truncated distribution object
This method is abstract : it has to be overriden
Parameters
----------
intervals : [(float, float)]
The intervals the distribution is truncated to
"""
self.intervals = intervals
dps = 15
not_precise = True
while not_precise:
Q = [self._cdf_notTruncated(a, b, dps) for a, b in intervals]
dps *= 2
not_precise = (fsum(Q) == 0.)
self._sumQ = fsum(Q)
self._dps = dps
self._Q = Q
def getNthPadovanNumber( arg ):
n = fadd( real( arg ), 4 )
a = root( fsub( fdiv( 27, 2 ), fdiv( fmul( 3, sqrt( 69 ) ), 2 ) ), 3 )
b = root( fdiv( fadd( 9, sqrt( 69 ) ), 2 ), 3 )
c = fadd( 1, fmul( mpc( 0, 1 ), sqrt( 3 ) ) )
d = fsub( 1, fmul( mpc( 0, 1 ), sqrt( 3 ) ) )
e = power( 3, fdiv( 2, 3 ) )
r = fadd( fdiv( a, 3 ), fdiv( b, e ) )
s = fsub( fmul( fdiv( d, -6 ), a ), fdiv( fmul( c, b ), fmul( 2, e ) ) )
t = fsub( fmul( fdiv( c, -6 ), a ), fdiv( fmul( d, b ), fmul( 2, e ) ) )
return nint( re( fsum( [ fdiv( power( r, n ), fadd( fmul( 2, r ), 3 ) ),
fdiv( power( s, n ), fadd( fmul( 2, s ), 3 ) ),
fdiv( power( t, n ), fadd( fmul( 2, t ), 3 ) ) ] ) ) )
def test_Matrix01(self):
a = mpmath.mpc(mpmath.pi,"0")
b = mpmath.mpc("0","1")
m = mpArray.mpArray([[a,b],[b,a]])
mat = mpArray.mpMatrix(m)
evals, evecs = mat.eigen(False, 'qeispack', verbose=True)
self.assertTrue(mpmath.fabs(mpmath.mpc(mpmath.pi,"1") - evals[0]) < 1e-32)
self.assertTrue(mpmath.fabs(mpmath.mpc(mpmath.pi,"-1") - evals[1]) < 1e-32)
self.assertTrue(numpy.all([mpmath.fabs(mpmath.mpf(1)/mpmath.sqrt("2") - mpmath.fabs(x)) < 1e-32 for x in evecs[0]]))
self.assertTrue(numpy.all([mpmath.fabs(mpmath.mpf(1)/mpmath.sqrt("2") - mpmath.fabs(x)) < 1e-32 for x in evecs[1]]))
self.assertTrue(mpmath.fabs(mpmath.fsum(evecs[0]*evecs[0].conj())) - mpmath.mpf(1) < 1e-32)
self.assertTrue(numpy.all([vec.abs2() -mpmath.mpf(1) < 1e-32 for vec in evecs]))
self.assertTrue(mpmath.fabs(evecs[0].inner(evecs[1])) < 1e-32)
def I_graph(m, µ, σ):
"""
Return two array x, y
representing the graph of I
(with mean value m, mean
log_pgen µ, var log_pgen σ)
"""
rg = np.linspace(0, 3 * m * µ, 1000)
S = [(k, scipy.stats.poisson.pmf(k, m)) for k in np.arange(1, max(int(3*m), 200))]
Is = [float(mpmath.fsum(1/mpmath.sqrt(2 * np.pi * σ**2 * k) *
mpmath.exp(-m) * mpmath.power(m, k) / mpmath.factorial(k) *
mpmath.exp(-(x - μ*k)**2/(2 * σ**2 * k))
for k, s in S if s > 1e-6))
+ (scipy.stats.poisson.pmf(0, m) if x == 0. else 0)
for x in rg]
return np.array(rg), np.array(Is)
def nll_hess(x, k, theta):
"""
Gamma distribution hessian of the negative log-likelihood function.
"""
_validate_k_theta(k, theta)
k = mpmath.mpf(k)
theta = mpmath.mpf(theta)
N = len(x)
sumx = mpmath.fsum(x)
# sumlnx = mpmath.fsum(mpmath.log(t) for t in x)
dk2 = -N*mpmath.psi(1, k)
dkdtheta = -N/theta
dtheta2 = -2*sumx/theta**3 + N*k/theta**2
return mpmath.matrix([[-dk2, -dkdtheta], [-dkdtheta, -dtheta2]])
def getSum( n ):
if isinstance( n, RPNGenerator ):
return getSum( list( n ) )
elif isinstance( n[ 0 ], ( list, RPNGenerator ) ):
return [ getSum( arg ) for arg in n ]
result = None
try:
result = fsum( n )
except:
result = n[ 0 ]
for i in n[ 1 : ]:
result = add( result, i )
return result
def calculateArithmeticMean( args ):
if isinstance( args, RPNGenerator ):
total = 0
count = 0
for i in args:
total += i
count += 1
return fdiv( total, count )
elif isinstance( args, list ):
if isinstance( args[ 0 ], ( list, RPNGenerator ) ):
return [ calculateArithmeticMean( list( arg ) ) for arg in args ]
else:
return fdiv( fsum( args ), len( args ) )
else:
return args
def getSum( n ):
if isinstance( n, RPNGenerator ):
return getSum( list( n ) )
if isinstance( n[ 0 ], ( list, RPNGenerator ) ):
return [ getSum( arg ) for arg in n ]
result = None
try:
result = fsum( n )
except TypeError:
result = n[ 0 ]
for i in n[ 1 : ]:
result = add( result, i )
return result
def boxcox_llf(lmb, x):
lmb = mpmath.mpf(lmb)
x = [mpmath.mpf(t) for t in x]
n = len(x)
logdata = [mpmath.log(t) for t in x]
sumlogdata = mpmath.fsum(logdata)
# Compute the variance of the transformed data.
if lmb == 0:
variance = var(logdata)
else:
# Transform without the constant offset 1/lmb. The offset does
# not effect the variance, and the subtraction of the offset can
# lead to loss of precision.
variance = var([t**lmb / lmb for t in x])
return (lmb - 1) * sumlogdata - n/2 * mpmath.log(variance)
def calculateRootMeanSquare( args ):
if isinstance( args, RPNGenerator ):
total = 0
count = 0
for i in args:
total += power( i, 2 )
count += 1
return square( fdiv( total, count ) )
elif isinstance( args, list ):
if isinstance( args[ 0 ], ( list, RPNGenerator ) ):
return [ calculateRootMeanSquare( list( arg ) ) for arg in args ]
elif isinstance( args[ 0 ], RPNMeasurement ):
pass # TODO: handle measurements
else:
return sqrt( fdiv( fsum( args, squared=True ), len( args ) ) )
else:
return args
def nll_invhess(x, k, theta):
"""
Gamma distribution inverse of the hessian of the negative log-likelihood.
"""
_validate_k_theta(k, theta)
k = mpmath.mpf(k)
theta = mpmath.mpf(theta)
N = len(x)
sumx = mpmath.fsum(x)
# sumlnx = mpmath.fsum(mpmath.log(t) for t in x)
dk2 = -N*mpmath.psi(1, k)
dkdtheta = -N/theta
dtheta2 = -2*sumx/theta**3 + N*k/theta**2
det = dk2*dtheta2 - dkdtheta**2
return mpmath.matrix([[-dtheta2/det, dkdtheta/det],
[dkdtheta/det, -dk2/det]])
def trapezium_rule(equation, lower_bound, upper_bound, n) -> str:
""" Given an equation, lower bound, upper bound and
number of strips, returns the area under a curve by
dividing the area into n trapezium and summing the
individual area.
>>> trapezium_rule([1, 0, 0], 0, 2, 100)
'2.6668'
>>> trapezium_rule([1, -2, 0, 2], -0.5, 2, 2000.5)
'3.56645978'
>>> trapezium_rule([1, -4, 3, 0], 0, 1, 1000)
'0.416665257'
"""
# Divide the total width by the number of division to get the width of each trapezium
trapezium_width = fdiv(
abs(fsub(upper_bound, lower_bound)), n
)
# Tabulates the temporary results by mapping each y to f(x)
ordinates_table = list(map(
lambda x: func(equation, x),
np.arange(
np.float64(lower_bound),
np.float64(upper_bound),
trapezium_width
)
))
ans = fmul(
fdiv(trapezium_width, 2),
fadd(
# Sum of the first and last ordinates
fadd(ordinates_table[0], ordinates_table[-1]),
fmul(2,
# Sum of the remaining ordinates
fsum(ordinates_table[1:-1]))
)
)
return str(abs(ans))
def calculateHeatIndexOperator( measurement1, measurement2 ):
'''
https://en.wikipedia.org/wiki/Heat_index#Formula
'''
# pylint: disable=invalid-name
validUnitTypes = [
[ 'temperature', 'constant' ],
]
arguments = matchUnitTypes( [ measurement1, measurement2 ], validUnitTypes )
if not arguments:
raise ValueError( '\'heat_index\' requires a temperature measurement and the relative humidity in percent' )
T = arguments[ 'temperature' ].convert( 'degrees_F' ).value
R = arguments[ 'constant' ]
if T < 80:
raise ValueError( '\'heat_index\' is not defined for temperatures less than 80 degrees fahrenheit' )
if R < 0.4 or R > 1.0:
raise ValueError( '\'heat_index\' requires a relative humidity value ranging from 40% to 100%' )
R = fmul( R, 100 )
c1 = -42.379
c2 = 2.04901523
c3 = 10.14333127
c4 = -0.22475541
c5 = -6.83783e-3
c6 = -5.481717e-2
c7 = 1.22874e-3
c8 = 8.5282e-4
c9 = -1.99e-6
heatIndex = fsum( [ c1, fmul( c2, T ), fmul( c3, R ), fprod( [ c4, T, R ] ), fprod( [ c5, T, T ] ),
fprod( [ c6, R, R ] ), fprod( [ c7, T, T, R ] ), fprod( [ c8, T, R, R ] ),
fprod( [ c9, T, T, R, R ] ) ] )
return RPNMeasurement( heatIndex, 'fahrenheit' ).convert( arguments[ 'temperature' ].units )
def asymptotic_expansion(self, omega):
# Evaluate the modulus of the characteristic function
domain = np.linspace(0, 5, 500)
char_fn = list(map(lambda t: mp.fabs(self.char_fn(t)), domain))
# thresh 1e-40
thresh_check = [
domain[i] for i in range(500) if char_fn[i] < mp.mpf(1e-50)
]
# Need to extend the domain
if len(list(thresh_check)) == 0:
j = 1
while len(list(thresh_check)) == 0:
domain = np.linspace(5 * j, 5 * (j + 1), 500)
char_fn = list(map(lambda t: mp.fabs(self.char_fn(t)), domain))
# thresh 1e-40
thresh_check = [
domain[i] for i in range(500) if char_fn[i] < mp.mpf(1e-50)
]
j += 1
cutoff = thresh_check[0]
# Generate the derivatives for the asymptotic expansion
order = 6
if not hasattr(self, 'diffs'):
self.gen_diffs(order)
# Evaluate the expansion
asym_series = mp.matrix(order, 1)
for i in range(1, order + 1):
asym_series[i - 1] = self.series_term(i, omega, cutoff)
# Sum up and take the real part
# We do not multiply by (-1) because the fact that we have g(x) = -x cancels this
return mp.re(mp.fsum(asym_series))
def logpmf(k, ntotal, ngood, nsample):
"""
Logarithm of the PMF of the hypergeometric distribution.
`logpmf` computes the natural logarithm of the probability mass function
of the hypergeometric distribution.
"""
_validate(ntotal, ngood, nsample)
nbad = ntotal - ngood
with mpmath.extradps(5):
# numerator terms
terms = [
mpmath.log(ntotal + 1),
logbeta(ntotal - nsample + 1, nsample + 1)
]
# denominator terms
terms.extend([
-mpmath.log(ngood + 1), -mpmath.log(nbad + 1),
-logbeta(k + 1, ngood - k + 1),
-logbeta(nsample - k + 1, nbad - nsample + k + 1)
])
return mpmath.fsum(terms)
def calculateRootMeanSquare( args ):
if isinstance( args, RPNGenerator ):
total = 0
count = 0
for i in args:
total += power( i, 2 )
count += 1
return square( fdiv( total, count ) )
if isinstance( args, list ):
if isinstance( args[ 0 ], ( list, RPNGenerator ) ):
return [ calculateRootMeanSquare( list( arg ) ) for arg in args ]
if isinstance( args[ 0 ], RPNMeasurement ):
# TODO: handle measurements
raise ValueError( '\'root_mean_square\' doesn\'t support measurements' )
return sqrt( fdiv( fsum( args, squared=True ), len( args ) ) )
return args
def calculateArithmeticMean( args ):
if isinstance( args, RPNGenerator ):
total = 0
count = 0
for i in args:
total += i
count += 1
return fdiv( total, count )
if isinstance( args, list ):
if isinstance( args[ 0 ], ( list, RPNGenerator ) ):
return [ calculateArithmeticMean( list( arg ) ) for arg in args ]
if isinstance( args[ 0 ], RPNMeasurement ):
# TODO: handle measurements
raise ValueError( '\'mean\' doesn\'t support measurements (yet)' )
return fdiv( fsum( args ), len( args ) )
return args
def getInvertedBits( n ):
value = real_int( n )
# determine how many groups of bits we will be looking at
if value == 0:
groupings = 1
else:
groupings = int( fadd( floor( fdiv( ( log( value, 2 ) ), g.bitwiseGroupSize ) ), 1 ) )
placeValue = mpmathify( 1 << g.bitwiseGroupSize )
multiplier = mpmathify( 1 )
remaining = value
result = mpmathify( 0 )
for i in range( 0, groupings ):
result = fadd( fmul( fsum( [ placeValue,
fneg( fmod( remaining, placeValue ) ), -1 ] ),
multiplier ), result )
remaining = floor( fdiv( remaining, placeValue ) )
multiplier = fmul( multiplier, placeValue )
return result
def calculateHeatIndex( measurement1, measurement2 ):
validUnitTypes = [
[ 'temperature', 'constant' ],
]
arguments = matchUnitTypes( [ measurement1, measurement2 ], validUnitTypes )
if not arguments:
raise ValueError( '\'heat_index\' requires a temperature measurement and the relative humidity in percent' )
T = arguments[ 'temperature' ].convert( 'degrees_F' ).value
R = arguments[ 'constant' ]
if T < 80:
raise ValueError( '\'heat_index\' is not defined for temperatures less than 80 degrees fahrenheit' )
if R < 0.4 or R > 1.0:
raise ValueError( '\'heat_index\' requires a relative humidity value ranging from 40% to 100%' )
R = fmul( R, 100 )
c1 = -42.379
c2 = 2.04901523
c3 = 10.14333127
c4 = -0.22475541
c5 = -6.83783e-3
c6 = -5.481717e-2
c7 = 1.22874e-3
c8 = 8.5282e-4
c9 = -1.99e-6
heatIndex = fsum( [ c1, fmul( c2, T ), fmul( c3, R ), fprod( [ c4, T, R ] ), fprod( [ c5, T, T ] ),
fprod( [ c6, R, R ] ), fprod( [ c7, T, T, R ] ), fprod( [ c8, T, R, R ] ),
fprod( [ c9, T, T, R, R ] ) ] )
return RPNMeasurement( heatIndex, 'fahrenheit' ).convert( arguments[ 'temperature' ].units )
def _mle_scale_func(scale, x, xbar):
emx = [mpmath.exp(-xi/scale) for xi in x]
s1 = mpmath.fsum([xi * emxi for xi, emxi in zip(x, emx)])
s2 = mpmath.fsum(emx)
return s2*(xbar - scale) - s1
def swap(self):
try:
i, h = self._next_random_swap()
except StopIteration:
self._debug('all swaps tried')
return False
self._debug('eval swap', i, h)
# try to swap medoid i with non-medoid h
clusters = self._clusters
distance = self._distance
# we differentiate fast_updates and slow_updates. fast_updates
# need to update only the second-nearest medoid. slow_updates
# need to update the nearest and second-nearest medoid.
fast_updates = []
def calculate_t():
# i attaches to a medoid
yield min(
distance(i, j) for j in chain(self._selected, [h]) if j != i)
# h detaches from its medoid
yield -distance(h, clusters[h][0])
# look at all other points
for j in self._unselected:
if j == h:
continue
# see [Ng1994] for a description of the following calculations
n1, n2 = clusters[j] # nearest two medoids
dh = distance(j, h) # d(Oj, Oh)
if n1 == i: # is j in cluster i?
d2 = distance(j, n2) # d(Oj, Oj,2)
if dh >= d2: # case (1); j does not go to h
yield d2 - distance(j, i)
fast_updates.append((j, n2))
else: # case (2); j goes to h
yield dh - distance(j, i)
fast_updates.append((j, h))
else:
k = clusters[j][0]
d2 = distance(j, k)
if dh >= d2: # case (3)
# j stays in current cluster. second nearest medoid
# to j might change with the introduction of h though.
fast_updates.append((j, k))
else: # case (4)
yield dh - d2
fast_updates.append((j, h))
t = fsum(calculate_t())
if t < 0: # swap is an improvement?
self._debug('ACCEPT swap t:%f' % t, i, h)
self._cost += t
selected = self._selected
del selected[selected.index(i)]
bisect.insort(selected, h)
slow_updates = [i] # update i's distances to medoids
for j, m in fast_updates:
if m == i:
slow_updates.append(j)
else:
min_d = None
min_k = None
for k in selected:
if k != m:
d = distance(k, j)
if min_d is None or d < min_d:
min_d = d
min_k = k
assert m != min_k and min_k is not None
clusters[j] = (m, min_k)
# update other second distances.
for _ in self._update_clusters(slow_updates):
pass # ignore distances (no influence on cost here).
# we swapped, so we want to allow previously used partners.
self._reset_random_swap()
return True
else:
return False
def eqn8(N, B):
sumterms = [power(B, n) / factorial(n) for n in range(int(N) + 1)]
return 1. / (exp(-B) * fsum(sumterms))
def fma(m, n, a):
list1 = []
for b in range(m + 1):
list1.append(
(a**(m * n + 1 + b) * (1 - a)**(m - b)) / factorial(m * n + b + 1))
return An(n)**m * factorial(m * n) * fsum(list1)
def apply(self, items, evaluation):
'Plus[items___]'
items = items.numerify(evaluation).get_sequence()
leaves = []
last_item = last_count = None
prec = min_prec(*items)
is_machine_precision = any(item.is_machine_precision() for item in items)
numbers = []
def append_last():
if last_item is not None:
if last_count == 1:
leaves.append(last_item)
else:
if last_item.has_form('Times', None):
last_item.leaves.insert(0, from_sympy(last_count))
leaves.append(last_item)
else:
leaves.append(Expression(
'Times', from_sympy(last_count), last_item))
for item in items:
if isinstance(item, Number):
numbers.append(item)
else:
count = rest = None
if item.has_form('Times', None):
for leaf in item.leaves:
if isinstance(leaf, Number):
count = leaf.to_sympy()
rest = item.leaves[:]
rest.remove(leaf)
if len(rest) == 1:
rest = rest[0]
else:
rest.sort()
rest = Expression('Times', *rest)
break
if count is None:
count = sympy.Integer(1)
rest = item
if last_item is not None and last_item == rest:
last_count = last_count + count
else:
append_last()
last_item = rest
last_count = count
append_last()
if numbers:
if prec is not None:
if is_machine_precision:
numbers = [item.to_mpmath() for item in numbers]
number = mpmath.fsum(numbers)
number = Number.from_mpmath(number)
else:
with mpmath.workprec(prec):
numbers = [item.to_mpmath() for item in numbers]
number = mpmath.fsum(numbers)
number = Number.from_mpmath(number, dps(prec))
else:
number = from_sympy(sum(item.to_sympy() for item in numbers))
else:
number = Integer(0)
if not number.same(Integer(0)):
leaves.insert(0, number)
if not leaves:
return Integer(0)
elif len(leaves) == 1:
return leaves[0]
else:
leaves.sort()
return Expression('Plus', *leaves)
def solveQuarticPolynomialOperator( _a, _b, _c, _d, _e ):
# pylint: disable=invalid-name
'''
This function applies the quartic formula to solve a polynomial
with coefficients of a, b, c, d, and e.
'''
if mp.dps < 50:
mp.dps = 50
# maybe it's really an order-3 polynomial
if _a == 0:
return solveCubicPolynomial( _b, _c, _d, _e )
# degenerate case, just return the two real and two imaginary 4th roots of the
# constant term divided by the 4th root of a
if _b == 0 and _c == 0 and _d == 0:
e = fdiv( _e, _a )
f = root( _a, 4 )
x1 = fdiv( root( fneg( e ), 4 ), f )
x2 = fdiv( fneg( root( fneg( e ), 4 ) ), f )
x3 = fdiv( mpc( 0, root( fneg( e ), 4 ) ), f )
x4 = fdiv( mpc( 0, fneg( root( fneg( e ), 4 ) ) ), f )
return [ x1, x2, x3, x4 ]
# otherwise we have a regular quartic to solve
b = fdiv( _b, _a )
c = fdiv( _c, _a )
d = fdiv( _d, _a )
e = fdiv( _e, _a )
# we turn the equation into a cubic that we can solve
f = fsub( c, fdiv( fmul( 3, power( b, 2 ) ), 8 ) )
g = fsum( [ d, fdiv( power( b, 3 ), 8 ), fneg( fdiv( fmul( b, c ), 2 ) ) ] )
h = fsum( [ e, fneg( fdiv( fmul( 3, power( b, 4 ) ), 256 ) ),
fmul( power( b, 2 ), fdiv( c, 16 ) ), fneg( fdiv( fmul( b, d ), 4 ) ) ] )
roots = solveCubicPolynomial( 1, fdiv( f, 2 ), fdiv( fsub( power( f, 2 ), fmul( 4, h ) ), 16 ),
fneg( fdiv( power( g, 2 ), 64 ) ) )
y1 = roots[ 0 ]
y2 = roots[ 1 ]
y3 = roots[ 2 ]
# pick two non-zero roots, if there are two imaginary roots, use them
if y1 == 0:
root1 = y2
root2 = y3
elif y2 == 0:
root1 = y1
root2 = y3
elif y3 == 0:
root1 = y1
root2 = y2
elif im( y1 ) != 0:
root1 = y1
if im( y2 ) != 0:
root2 = y2
else:
root2 = y3
else:
root1 = y2
root2 = y3
# more variables...
p = sqrt( root1 )
q = sqrt( root2 )
r = fdiv( fneg( g ), fprod( [ 8, p, q ] ) )
s = fneg( fdiv( b, 4 ) )
# put together the 4 roots
x1 = fsum( [ p, q, r, s ] )
x2 = fsum( [ p, fneg( q ), fneg( r ), s ] )
x3 = fsum( [ fneg( p ), q, fneg( r ), s ] )
x4 = fsum( [ fneg( p ), fneg( q ), r, s ] )
return [ chop( x1 ), chop( x2 ), chop( x3 ), chop( x4 ) ]
def _kmeans(self, k):
# implements an improved version of kmeans, see [Hamerly2010].
x = self.x
d = self.d
assert k <= len(x)
# pick initial clusters. actually quite an important step.
c = list(islice(self._pick_initial(), 0, k))
assert len(c) == k
q = [0] * len(c)
cc = [[0] * len(x[0]) for _ in range(k)]
a = [0] * len(x)
u = [0] * len(x)
l = [0] * len(x)
for i, xi in enumerate(x):
ai, u[i], _, l[i] = _smallest2(d(xi, cj) for cj in c)
q[ai] += 1
cc[ai] = _pairwise_sum(cc[ai], xi)
a[i] = ai
s = [0] * len(c)
p = [0] * len(c)
change = None
while change is None or change > self.epsilon:
# find cluster distances
cd = self._distances(c)
s = [
min(cd(j1, j2) for j2 in range(k) if j2 != j1)
for j1 in range(k)
]
# find new assignments
for i, ai in enumerate(a):
m = max(s[ai] / 2., l[i])
if u[i] > m:
xi = x[i]
u[i] = d(xi, c[ai])
if u[i] > m:
new_ai, u[i], _, l[i] = _smallest2(
d(xi, cj) for cj in c)
if new_ai != ai:
q[ai] -= 1
q[new_ai] += 1
cc[ai] = [a - b for a, b in zip(cc[ai], xi)]
cc[new_ai] = [
a + b for a, b in zip(cc[new_ai], xi)
]
a[i] = new_ai
# move centers
empty_cluster = False
for j in range(len(c)):
qj = q[j]
if qj == 0:
empty_cluster = True
break
c_old = c[j]
c_new = [ccj / qj for ccj in cc[j]]
distance = d(c_old, c_new)
c[j] = c_new
p[j] = distance
if empty_cluster:
break
# update bounds
r1, p1, r2, p2 = _largest2(p)
for i, ai in enumerate(a):
u[i] += p[ai]
if r1 == ai:
l[i] -= p2
else:
l[i] -= p1
change = sum(p)
# compute an approximate silhouette index
within = [0] * len(c)
for i, ai in enumerate(a):
within[ai] += d(x[i], c[ai])
for j in range(len(c)):
if q[j] == 1:
return a, -1. # no good config
within[j] /= q[j] - 1
silhouette = fsum(_silhouette(a, b)
for a, b in zip(within, s)) / len(c)
return a, silhouette
