def SetMultinormalInitialPoints(self, mean, var=None):
"""Generate Initial Points from Multivariate Normal.
input::
- mean must be a sequence of length self.nDim
- var can be...
None: -> it becomes the identity
scalar: -> var becomes scalar * I
matrix: -> the variance matrix. must be the right size!
"""
from mystic.tools import random_state
rng = random_state(module='numpy.random')
assert (len(mean) == self.nDim)
if var is None:
var = numpy.eye(self.nDim)
else:
try: # scalar ?
float(var)
except: # nope. var better be matrix of the right size (no check)
pass
else:
var = var * numpy.eye(self.nDim)
for i in range(len(self.population)):
self.population[i] = rng.multivariate_normal(mean, var).tolist()
return
def SetMultinormalInitialPoints(self, mean, var = None):
"""Generate Initial Points from Multivariate Normal.
input::
- mean must be a sequence of length self.nDim
- var can be...
None: -> it becomes the identity
scalar: -> var becomes scalar * I
matrix: -> the variance matrix. must be the right size!
"""
from mystic.tools import random_state
prng = random_state(module='numpy.random')
assert(len(mean) == self.nDim)
if var is None:
var = numpy.eye(self.nDim)
else:
try: # scalar ?
float(var)
except: # nope. var better be matrix of the right size (no check)
pass
else:
var = var * numpy.eye(self.nDim)
for i in range(len(self.population)):
self.population[i] = prng.multivariate_normal(mean, var).tolist()
return
def randomly_bin(N, ndim=None, ones=True, exact=True):
"""
generate N bins randomly gridded across ndim dimensions
Inputs:
N -- integer number of bins, where N = prod(bins)
ndim -- integer length of bins, thus ndim = len(bins)
ones -- if False, prevent bins from containing "1s", wherever possible
exact -- if False, find N-1 bins for prime numbers
"""
if ndim == 0: return []
if N == 0: return [0] if ndim else [0] * ndim
from itertools import chain
from mystic.tools import random_state
try:
xrange
except NameError:
xrange = range
random = random_state().random
def factors(n):
result = list()
for i in chain([2], xrange(3, n + 1, 2)):
s = 0
while n % i == 0:
n //= i
s += 1
result.extend([i] * s)
if n == 1:
return result
result = factors(N)
dim = nfact = len(result)
prime = nfact == 1
if ndim:
result += [1] * (ndim - (nfact // ndim))
dim = ndim
elif ones:
result += [1] # add some 'randomness' by adding a "1"
# if ones, mix in the 1s; otherwise, only use 1s when ndim < len(result)
if ones: result = sorted(result, key=lambda v: random())
else: result[:nfact] = sorted(result[:nfact], key=lambda v: random())
from numpy import product
result = [product(result[i::dim]) for i in range(dim)]
# if not ones, now needs a full sort to sort in the 1s
if not ones: result = sorted(result, key=lambda v: random())
elif not ndim and 1 in result: result.remove(1) # remove the added "1"
# if it's a prime, then do N-1 if exact=False
if not exact and N > 3 and prime:
result = randomly_bin(N - 1, ndim, ones)
return result
def _random_samples(lb,ub,npts=10000):
"""
generate npts random samples between given lb & ub
Inputs:
lower bounds -- a list of the lower bounds
upper bounds -- a list of the upper bounds
npts -- number of sample points [default = 10000]
"""
from mystic.tools import random_state
dim = len(lb)
pts = random_state(module='numpy.random').rand(dim,npts)
for i in range(dim):
pts[i] = (pts[i] * abs(ub[i] - lb[i])) + lb[i]
return pts #XXX: returns a numpy.array
def _random_samples(lb, ub, npts=10000):
"""
generate npts random samples between given lb & ub
Inputs:
lower bounds -- a list of the lower bounds
upper bounds -- a list of the upper bounds
npts -- number of sample points [default = 10000]
"""
from mystic.tools import random_state
dim = len(lb)
pts = random_state(module='numpy.random').rand(dim, npts)
for i in range(dim):
pts[i] = (pts[i] * abs(ub[i] - lb[i])) + lb[i]
return pts #XXX: returns a numpy.array
def randomly_bin(N, ndim=None, ones=True, exact=True):
"""
generate N bins randomly gridded across ndim dimensions
Inputs:
N -- integer number of bins, where N = prod(bins)
ndim -- integer length of bins, thus ndim = len(bins)
ones -- if False, prevent bins from containing "1s", wherever possible
exact -- if False, find N-1 bins for prime numbers
"""
if ndim == 0: return []
if N == 0: return [0] if ndim else [0]*ndim
from itertools import chain
from mystic.tools import random_state
try:
xrange
except NameError:
xrange = range
random = random_state().random
def factors(n):
result = list()
for i in chain([2],xrange(3,n+1,2)):
s = 0
while n%i == 0:
n //= i
s += 1
result.extend([i]*s)
if n == 1:
return result
result = factors(N)
dim = nfact = len(result)
prime = nfact == 1
if ndim: result += [1] * (ndim - (nfact // ndim)); dim = ndim
elif ones: result += [1] # add some 'randomness' by adding a "1"
# if ones, mix in the 1s; otherwise, only use 1s when ndim < len(result)
if ones: result = sorted(result, key=lambda v: random())
else: result[:nfact] = sorted(result[:nfact], key=lambda v: random())
from numpy import product
result = [product(result[i::dim]) for i in range(dim)]
# if not ones, now needs a full sort to sort in the 1s
if not ones: result = sorted(result, key=lambda v: random())
elif not ndim and 1 in result: result.remove(1) # remove the added "1"
# if it's a prime, then do N-1 if exact=False
if not exact and N > 3 and prime:
result = randomly_bin(N-1, ndim, ones)
return result
def weighted_select(samples, weights, mass=1.0):
"""randomly select a sample from weighted set of samples
Inputs:
samples -- a list of sample points
weights -- a list of sample weights
mass -- sum of normalized weights
"""
from numpy import sum, array
from mystic.tools import random_state
rand = random_state().random
# generate a list representing the weighted distribution
wts = normalize(weights, mass)
wts = array([sum(wts[:i + 1]) for i in range(len(wts))])
# correct for any rounding error
wts[-1] = mass
# generate a random weight
w = mass * rand()
# select samples that corresponds to randomly selected weight
selected = len(wts[wts <= w])
return samples[selected]
def weighted_select(samples, weights, mass=1.0):
"""randomly select a sample from weighted set of samples
Inputs:
samples -- a list of sample points
weights -- a list of sample weights
mass -- sum of normalized weights
"""
from numpy import sum, array
from mystic.tools import random_state
rand = random_state().random
# generate a list representing the weighted distribution
wts = normalize(weights, mass)
wts = array([sum(wts[:i+1]) for i in range(len(wts))])
# correct for any rounding error
wts[-1] = mass
# generate a random weight
w = mass * rand()
# select samples that corresponds to randomly selected weight
selected = len(wts[ wts <= w ])
return samples[selected]
def __init__(self, generator=None, *args, **kwds):
"""
generate a sampling distribution with interface dist(size=None)
input::
- generator: a 'distribution' method from scipy.stats or numpy.random
- args: positional arguments for the distribtution object
- kwds: keyword arguments for the distribution object
note::
this method only accepts numpy.random methods with the keyword 'size'
"""
from mystic.tools import random_state
rng = random_state(module='numpy.random')
if generator is None: generator = rng.random
if getattr(generator, 'rvs', False):
d = generator(*args, **kwds)
self.rvs = lambda size=None: d.rvs(size=size, random_state=rng)
else:
d = getattr(rng, generator.__name__)
self.rvs = lambda size=None: d(size=size, *args, **kwds)
return
def __init__(self, generator=None, *args, **kwds):
"""
generate a sampling distribution with interface dist(size=None)
input::
- generator: a 'distribution' method from scipy.stats or numpy.random
- args: positional arguments for the distribtution object
- kwds: keyword arguments for the distribution object
note::
this method only accepts numpy.random methods with the keyword 'size'
"""
from mystic.tools import random_state
rng = random_state(module='numpy.random')
if generator is None: generator = rng.random
if getattr(generator, 'rvs', False):
d = generator(*args, **kwds)
self.rvs = lambda size=None: d.rvs(size=size, random_state=rng)
else:
d = getattr(rng, generator.__name__)
self.rvs = lambda size=None: d(size=size, *args, **kwds)
return
def scem(Ck, ak, Sk, Sak, target, cn):
"""
This is the SCEM algorithm starting from line [35] of the reference [1].
- [inout] Ck is the kth 'complex' with m points. This should be an m by n array
n being the dimensionality of the density function. i.e., the data
are arranged in rows.
Ck is assumed to be sorted according to the target density.
- [inout] ak, the density of the points of Ck.
- [inout] Sk, the entire chain. (should be a list)
- [inout] Sak, the cost of the entire chain (should be a list)
Sak would be more convenient to use if it is a numpy array, but we need
to append to it frequently.
- [in] target: target density function
- [in] cn: jumprate. (see Paragraph 37 of [1.]
- The invariants: ak is always aligned with Ck, and are the cost of Ck
- Similarly, Sak is always aligned with Sk in the same way.
- On return... sort order in Ck/ak is destroyed. but see sort_complex2
"""
import numpy
from mystic.tools import random_state
prng = random_state(module=numpy.random)
# function level constants
T = 100000. # predefined likelihood ratio. Paragraph 45 of [1.]
# Sort Ck according to ak
#Ck, ak = sort_complex0(Ck, ak)
#print("ak before: %s" % ak)
#Ck, ak = sort_complex(Ck, ak)
sort_complex2(Ck, ak)
#print("ak after: %s" % ak)
# number of points per complex
M = Ck.shape[0]
mu = numpy.mean(Ck,0) # row mean
# (numpy.cov takes data in columns)
Sigma = numpy.cov(numpy.transpose(Ck))
# Gamma (line 35 of [1]. Best to Worst)
Gamma = ak[0] / (ak[-1]+TINY)
if len(Sak) >= M:
meansak = numpy.mean(Sak[-M:])
else:
meansak = numpy.mean(Sak)
alpha_k = numpy.mean(ak) / (meansak+TINY)
if alpha_k < T:
# Paragraph 37 of [1]
basept = Sk[-1]
else: # numpy.mean(asak) is very close to zero.
# Paragraph 38 of [1]
basept = mu
# TODO should take a proposal instead !
Yt = prng.multivariate_normal(basept, cn*cn * Sigma)
cY = target(Yt)
# print("new/orig : %s %s" % (cY, Sak[-1]))
r = min( cY / (Sak[-1]+TINY), 1)
if prng.rand() <= r:
Sk.append(Yt)
Sak.append(cY)
# Paragraph 43 of [1] (update the best of Ck)
Ck[0], ak[0] = Sk[-1], Sak[-1]
else:
Sk.append(Sk[-1])
Sak.append(Sak[-1])
if Gamma > T and Sak[-1] > ak[-1]:
# Paragraph 43 of [1] (update the worst of Ck)
Ck[-1], ak[-1] = Sk[-1], Sak[-1]
# mainly because of the logic in Paragraph [43] that updates the complex,
# this function is not "functional" and modifies its argument instead.
# hence no return value
return
def scem(Ck, ak, Sk, Sak, target, cn):
"""
This is the SCEM algorithm starting from line [35] of the reference [1].
- [inout] Ck is the kth 'complex' with m points. This should be an m by n array
n being the dimensionality of the density function. i.e., the data
are arranged in rows.
Ck is assumed to be sorted according to the target density.
- [inout] ak, the density of the points of Ck.
- [inout] Sk, the entire chain. (should be a list)
- [inout] Sak, the cost of the entire chain (should be a list)
Sak would be more convenient to use if it is a numpy array, but we need
to append to it frequently.
- [in] target: target density function
- [in] cn: jumprate. (see Paragraph 37 of [1.]
- The invariants: ak is always aligned with Ck, and are the cost of Ck
- Similarly, Sak is always aligned with Sk in the same way.
- On return... sort order in Ck/ak is destroyed. but see sort_complex2
"""
import numpy
from mystic.tools import random_state
prng = random_state(module=numpy.random)
# function level constants
T = 100000. # predefined likelihood ratio. Paragraph 45 of [1.]
# Sort Ck according to ak
#Ck, ak = sort_complex0(Ck, ak)
#print("ak before: %s" % ak)
#Ck, ak = sort_complex(Ck, ak)
sort_complex2(Ck, ak)
#print("ak after: %s" % ak)
# number of points per complex
M = Ck.shape[0]
mu = numpy.mean(Ck,0) # row mean
# (numpy.cov takes data in columns)
Sigma = numpy.cov(numpy.transpose(Ck))
# Gamma (line 35 of [1]. Best to Worst)
Gamma = ak[0] / (ak[-1]+TINY)
if len(Sak) >= M:
meansak = numpy.mean(Sak[-M:])
else:
meansak = numpy.mean(Sak)
alpha_k = numpy.mean(ak) / (meansak+TINY)
if alpha_k < T:
# Paragraph 37 of [1]
basept = Sk[-1]
else: # numpy.mean(asak) is very close to zero.
# Paragraph 38 of [1]
basept = mu
# TODO should take a proposal instead !
Yt = prng.multivariate_normal(basept, cn*cn * Sigma)
cY = target(Yt)
# print("new/orig : %s %s" % (cY, Sak[-1]))
r = min( cY / (Sak[-1]+TINY), 1)
if prng.rand() <= r:
Sk.append(Yt)
Sak.append(cY)
# Paragraph 43 of [1] (update the best of Ck)
Ck[0], ak[0] = Sk[-1], Sak[-1]
else:
Sk.append(Sk[-1])
Sak.append(Sak[-1])
if Gamma > T and Sak[-1] > ak[-1]:
# Paragraph 43 of [1] (update the worst of Ck)
Ck[-1], ak[-1] = Sk[-1], Sak[-1]
# mainly because of the logic in Paragraph [43] that updates the complex,
# this function is not "functional" and modifies its argument instead.
# hence no return value
return