def is_posdefinite(matrix):
"""
The test for positive definiteness using the determinants of the nested
principal minor matrices is taken from Varian; "Microeconomic Analysis".
Returns True if input matrix is positive definite, False otherwise.
"""
flag = True
ndim = squaredim(matrix, 'is_posdefinite')
for k in range(0, ndim):
'''# Test No. 1 - Necessary condition for positive SEMI-definiteness:
if matrix[k][k] <= 0.0:
flag = False
break'''
# (Test No. 2 -) Sufficient condition for positive definiteness:
minor = Matrix()
kp1 = k + 1
minor.zero(kp1, kp1)
for j in range(0, kp1):
for i in range(0, kp1): minor[j][i] = matrix[j][i]
x = determinant(minor)
del minor
if x <= 0.0:
flag = False
break
return flag
def ludcmp_chol(matrix, test=False):
"""
Decomposes/factorizes square, positive definite input matrix into
one lower and one upper matrix. The upper matrix is the transpose of
the lower matrix.
NB. It only works on square, symmetric, positive definite matrices!!!
"""
if test:
errortext1 = "Input matrix not positive definite in ludcmp_chol!"
assert is_posdefinite(matrix), errortext1
errortext2 = "Input matrix not symmetric in ludcmp_chol!"
assert is_symmetrical(matrix), errortext2
ndim = squaredim(matrix, 'ludcmp_chol')
# Create new square matrix of the same size as the input matrix:
clower = Matrix()
clower.zero(ndim, ndim)
# Perform the necessary manipulations:
for k in range(0, ndim):
kp1 = k + 1
for j in range(0, kp1):
summ = 0.0
for i in range(0, j): summ += clower[k][i]*clower[j][i]
if j == k: clower[k][j] = sqrt(matrix[k][j] - summ)
else: clower[k][j] = (matrix[k][j]-summ) / float(clower[j][j])
clowert = transposed(clower)
return clower, clowert
def is_posdefinite(matrix):
"""
The test for positive definiteness using the determinants of the nested
principal minor matrices is taken from Varian; "Microeconomic Analysis".
Returns True if input matrix is positive definite, False otherwise.
"""
flag = True
ndim = squaredim(matrix, 'is_posdefinite')
for k in range(0, ndim):
'''# Test No. 1 - Necessary condition for positive SEMI-definiteness:
if matrix[k][k] <= 0.0:
flag = False
break'''
# (Test No. 2 -) Sufficient condition for positive definiteness:
minor = Matrix()
kp1 = k + 1
minor.zero(kp1, kp1)
for j in range(0, kp1):
for i in range(0, kp1):
minor[j][i] = matrix[j][i]
x = determinant(minor)
del minor
if x <= 0.0:
flag = False
break
return flag
def ludcmp_chol(matrix, test=False):
"""
Decomposes/factorizes square, positive definite input matrix into
one lower and one upper matrix. The upper matrix is the transpose of
the lower matrix.
NB. It only works on square, symmetric, positive definite matrices!!!
"""
if test:
errortext1 = "Input matrix not positive definite in ludcmp_chol!"
assert is_posdefinite(matrix), errortext1
errortext2 = "Input matrix not symmetric in ludcmp_chol!"
assert is_symmetrical(matrix), errortext2
ndim = squaredim(matrix, 'ludcmp_chol')
# Create new square matrix of the same size as the input matrix:
clower = Matrix()
clower.zero(ndim, ndim)
# Perform the necessary manipulations:
for k in range(0, ndim):
kp1 = k + 1
for j in range(0, kp1):
summ = 0.0
for i in range(0, j):
summ += clower[k][i] * clower[j][i]
if j == k: clower[k][j] = sqrt(matrix[k][j] - summ)
else: clower[k][j] = (matrix[k][j] - summ) / float(clower[j][j])
clowert = transposed(clower)
return clower, clowert
def _jake3(self, t, y, hf=0.5**20, ha=0.5**40):
"""
Auxiliary function/method used by implicit methods to compute
the Jacobian. Cannot be used for dicts!!!!!
"""
yplus = array('d', [])
yminus = array('d', [])
for n in self._sequence:
why = y[n]
yplus.append( (1.0 + hf) * why + ha)
yminus.append((1.0 - hf) * why - ha)
jacob = Matrix()
for n in self._sequence:
derivs = array('d', [])
for m in self._sequence:
yn = deepcopy(y)
yp = yplus[m]
yn[m] = yp
fp = self._model(t, yn)[n]
ym = yminus[m]
yn[m] = ym
fm = self._model(t, yn)[n]
deriv = (fp-fm) / (yp-ym)
derivs.append(deriv)
jacob.append(derivs)
return jacob
def _fidfi(y):
# fi first
f = self._model(tnext, y)
fi = deepcopy(f)
beta = deepcopy(fi)
for n in self._sequence:
fi[n] = 137.0*y[n] - 300.0*s[n] + \
300.0*self.__prev[3][n] - \
200.0*self.__prev[2][n] + \
75.0*self.__prev[1][n] - \
12.0*self.__prev[0][n] - 60.0*h*f[n]
beta[n] = - fi[n]
# then fid = dfi[n]/dy[m] = 137*dy[n]/dy[m] - 60*h*df[n]/dy[m],
# or - 60*h*df[n]/dy[m]; n != m, and
# 137 - 60*h*df[n]/dy[m]; n == m
jacob = self._jake3(tnext, y, hf, ha)
fid = Matrix()
for n in self._sequence:
derivs = array('d', [])
for m in self._sequence:
deriv = 137.0*krond(n, m) - 60.0*h*jacob[n][m]
derivs.append(deriv)
fid.append(derivs)
alpha = Matrix(fid)
return alpha, beta
def antithet_sample(self, nparams):
"""
Generates a matrix having two rows, the first row being a list of
uniformly distributed random numbers p in [0.0, 1.0], each row
containing nparams elements. The second row contains the corresponding
antithetic sample with the complements 1-p.
"""
rstream = self.rstream
antimatrix = Matrix() # antimatrix belongs to the Matrix class
for k in range(0, nparams):
pvector = array('d', [])
p1 = rstream.runif01()
pvector.append(p1)
dum = rstream.runif01() # For synchronization only - never used
p2 = 1.0 - p1
p2 = kept_within(0.0, p2, 1.0) # Probabilities must be in [0.0, 1.0]
pvector.append(p2)
antimatrix.append(pvector)
# Matrix must be transposed in order for each sample to occupy one row.
# Sample vector k is in antimatrix[k], where k is 0 or 1
antimatrix.transpose()
return antimatrix
def scaled(matrix, scalar):
"""
Multiply matrix by scalar.
"""
sized(matrix, 'scaled')
copymx = deepcopy(matrix)
return Matrix(xmap((lambda x: scalar * x), copymx))
def _fidfi(y):
# fi first
f = self._model(tnext, y)
fi = deepcopy(f)
beta = deepcopy(fi)
for n in self._sequence:
fi[n] = y[n] - s[n] - h*f[n]
beta[n] = - fi[n]
# then fid = dfi[n]/dy[m] = dy[n]/dy[m] - h*df[n]/dy[m], or
# - h*df[n]/dy[m]; n != m, and
# 1.0 - h*df[n]/dy[m]; n == m
jacob = self._jake3(tnext, y, hf, ha)
fid = Matrix()
for n in self._sequence:
derivs = array('d', [])
for m in self._sequence:
deriv = 1.0*krond(n, m) - h*jacob[n][m]
derivs.append(deriv)
fid.append(derivs)
alpha = Matrix(fid)
return alpha, beta
def antithet_sample(self, nparams):
"""
Generates a matrix having two rows, the first row being a list of
uniformly distributed random numbers p in [0.0, 1.0], each row
containing nparams elements. The second row contains the corresponding
antithetic sample with the complements 1-p.
"""
rstream = self.rstream
antimatrix = Matrix() # antimatrix belongs to the Matrix class
for k in range(0, nparams):
pvector = array('d', [])
p1 = rstream.runif01()
pvector.append(p1)
dum = rstream.runif01() # For synchronization only - never used
p2 = 1.0 - p1
p2 = kept_within(0.0, p2,
1.0) # Probabilities must be in [0.0, 1.0]
pvector.append(p2)
antimatrix.append(pvector)
# Matrix must be transposed in order for each sample to occupy one row.
# Sample vector k is in antimatrix[k], where k is 0 or 1
antimatrix.transpose()
return antimatrix
def ludcmp_crout(matrix):
"""
Decomposes/factorizes square input matrix into a lower and an
upper matrix using Crout's algorithm WITHOUT pivoting.
NB. It only works for square matrices!!!
"""
ndim = squaredim(matrix, 'ludcmp_crout')
# Copy object instance to new matrix in order for the original instance
# not to be destroyed.
# Create two new square matrices of the same sized as the input matrix:
# one unity matrix (to be the lower matrix), one zero matrix (to be
# the upper matrix)
copymx = deepcopy(matrix)
lower = Matrix()
lower.unity(ndim)
upper = Matrix()
upper.zero(ndim, ndim)
permlist = list(range(0, ndim))
# Perform the necessary manipulations:
for j in range(0, ndim):
iu = 0
while iu <= j:
k = 0
summ = 0.0
while k < iu:
summ += lower[iu][k] * upper[k][j]
k = k + 1
upper[iu][j] = copymx[iu][j] - summ
iu = iu + 1
il = j + 1
while il < ndim:
k = 0
summ = 0.0
while k < j:
summ += lower[il][k] * upper[k][j]
k = k + 1
divisor = float(upper[j][j])
if abs(divisor) < TINY: divisor = fsign(divisor) * TINY
lower[il][j] = (copymx[il][j] - summ) / divisor
il = il + 1
parity = 1.0
return lower, upper, permlist, parity
def _fidfi(y):
# fi first
f = self._model(tnext, y)
fi = deepcopy(f)
beta = deepcopy(fi)
for n in self._sequence:
fi[n] = 25.0*y[n] - 48.0*s[n] + 36.0*self.__prev[2][n] - \
16.0*self.__prev[1][n] + \
3.0*self.__prev[0][n] - 12.0*h*f[n]
beta[n] = - fi[n]
# then fid = dfi[n]/dy[m] = 3*dy[n]/dy[m] - 2*h*df[n]/dy[m], or
# - 12*h*df[n]/dy[m]; n != m, and
# 25 - 12*h*df[n]/dy[m]; n == m
jacob = self._jake3(tnext, y, hf, ha)
fid = Matrix()
for n in self._sequence:
derivs = array('d', [])
for m in self._sequence:
deriv = 25.0*krond(n, m) - 12.0*h*jacob[n][m]
derivs.append(deriv)
fid.append(derivs)
alpha = Matrix(fid)
return alpha, beta
def corrmatrix(inputmatrix):
"""
Computes the correlation matrix of the input matrix. Each row is assumed
to contain the vector for one parameter.
"""
ndim = len(inputmatrix) # = the number of rows/parameters
# First create unity output matrix
corrmatrix = Matrix()
corrmatrix.unity(ndim)
# Then fill it with correlation coefficients
for k in range(0, ndim):
kp1 = k + 1
for j in range(0, kp1):
if j != k:
#amk,amj,vk,vj,covkj, rhokj = covar(inputmatrix[k], \
# inputmatrix[j])
#corrmatrix[k][j] = corrmatrix[j][k] = rhokj
corrmatrix[k][j] = corrmatrix[j][k] = \
covar(inputmatrix[k], inputmatrix[j])[5] # = rhokj
return corrmatrix
def corrmatrix(inputmatrix):
"""
Computes the correlation matrix of the input matrix. Each row is assumed
to contain the vector for one parameter.
"""
ndim = len(inputmatrix) # = the number of rows/parameters
# First create unity output matrix
corrmatrix = Matrix()
corrmatrix.unity(ndim)
# Then fill it with correlation coefficients
for k in range(0, ndim):
kp1 = k + 1
for j in range(0, kp1):
if j != k:
#amk,amj,vk,vj,covkj, rhokj = covar(inputmatrix[k], \
# inputmatrix[j])
#corrmatrix[k][j] = corrmatrix[j][k] = rhokj
corrmatrix[k][j] = corrmatrix[j][k] = \
covar(inputmatrix[k], inputmatrix[j])[5] # = rhokj
return corrmatrix
def transposed(matrix):
"""
Transpose matrix.
"""
nrows, ncols = sized(matrix, 'transposed')
newmatrix = ncols * [float('nan')]
for k in range(0, ncols): # List comprehension used for the innermost loop
newmatrix[k] = array('d', [row[k] for row in matrix])
tmatrix = Matrix(newmatrix)
del newmatrix
'''tmatrix = Matrix(matrix)
tmatrix.transpose() # would be slower'''
return tmatrix
def inverted(matrix, pivoting=True):
"""
Only square matrices can be inverted!
"""
ndim = squaredim(matrix, 'inverted')
# First: LU-decompose matrix to be inverted
if pivoting:
lower, upper, permlist, parity = ludcmp_crout_piv(matrix)
else:
lower, upper, permlist, parity = ludcmp_crout(matrix)
# Create unity matrix
unitymatrix = Matrix()
unitymatrix.unity(ndim)
# Loop over the columns in unity matrix and substitute
# (uses the fact that rows and columns are the same in a unity matrix)
columns = Matrix()
columns.zero(ndim, ndim)
for k in range(0, ndim):
columns[k] = lusubs(lower, upper, unitymatrix[k], permlist)
# preparations below for changing lusubs to handling column vector
# instead of list
#row = Matrix([unitymatrix[k]])
#column = transpose(row)
#columns[k] = lusubs(lower, upper, column, permlist)
#del column
# Transpose matrix to get inverse
newmatrix = ndim * [float('nan')]
for k in range(0,
ndim): # List comprehension is used for the innermost loop
newmatrix[k] = array('d', [row[k] for row in columns])
imatrix = Matrix(newmatrix)
del newmatrix
return imatrix
def ludcmp_crout(matrix):
"""
Decomposes/factorizes square input matrix into a lower and an
upper matrix using Crout's algorithm WITHOUT pivoting.
NB. It only works for square matrices!!!
"""
ndim = squaredim(matrix, 'ludcmp_crout')
# Copy object instance to new matrix in order for the original instance
# not to be destroyed.
# Create two new square matrices of the same sized as the input matrix:
# one unity matrix (to be the lower matrix), one zero matrix (to be
# the upper matrix)
copymx = deepcopy(matrix)
lower = Matrix()
lower.unity(ndim)
upper = Matrix()
upper.zero(ndim, ndim)
permlist = list(range(0, ndim))
# Perform the necessary manipulations:
for j in range(0, ndim):
iu = 0
while iu <= j:
k = 0
summ = 0.0
while k < iu:
summ += lower[iu][k]*upper[k][j]
k = k + 1
upper[iu][j] = copymx[iu][j] - summ
iu = iu + 1
il = j + 1
while il < ndim:
k = 0
summ = 0.0
while k < j:
summ += lower[il][k]*upper[k][j]
k = k + 1
divisor = float(upper[j][j])
if abs(divisor) < TINY: divisor = fsign(divisor)*TINY
lower[il][j] = (copymx[il][j]-summ) / divisor
il = il + 1
parity = 1.0
return lower, upper, permlist, parity
def inverted(matrix, pivoting=True):
"""
Only square matrices can be inverted!
"""
ndim = squaredim(matrix, 'inverted')
# First: LU-decompose matrix to be inverted
if pivoting:
lower, upper, permlist, parity = ludcmp_crout_piv(matrix)
else:
lower, upper, permlist, parity = ludcmp_crout(matrix)
# Create unity matrix
unitymatrix = Matrix()
unitymatrix.unity(ndim)
# Loop over the columns in unity matrix and substitute
# (uses the fact that rows and columns are the same in a unity matrix)
columns = Matrix()
columns.zero(ndim, ndim)
for k in range(0, ndim):
columns[k] = lusubs(lower, upper, unitymatrix[k], permlist)
# preparations below for changing lusubs to handling column vector
# instead of list
#row = Matrix([unitymatrix[k]])
#column = transpose(row)
#columns[k] = lusubs(lower, upper, column, permlist)
#del column
# Transpose matrix to get inverse
newmatrix = ndim*[float('nan')]
for k in range(0, ndim): # List comprehension is used for the innermost loop
newmatrix[k] = array('d', [row[k] for row in columns])
imatrix = Matrix(newmatrix)
del newmatrix
return imatrix
def ludcmp_crout_piv(matrix):
"""
Decomposes/factorizes square input matrix into a lower
and an upper matrix using Crout's algorithm WITH pivoting.
NB. It only works on square matrices!!!
"""
ndim = squaredim(matrix, 'ludcmp_crout_piv')
ndm1 = ndim - 1
vv = array('d', ndim * [0.0])
permlist = list(range(0, ndim))
parity = 1.0
imax = 0
# Copy to matrix to be processed (maintains the original matrix intact)
compactlu = deepcopy(matrix)
for i in range(0, ndim): # Copy and do some other stuff
big = 0.0
for j in range(0, ndim):
temp = abs(compactlu[i][j])
if temp > big: big = temp
assert big > 0.0
vv[i] = 1.0 / big
# Perform the necessary manipulations:
for j in range(0, ndim):
for i in range(0, j):
sum = compactlu[i][j]
for k in range(0, i):
sum -= compactlu[i][k] * compactlu[k][j]
compactlu[i][j] = sum
big = 0.0
for i in range(j, ndim):
sum = compactlu[i][j]
for k in range(0, j):
sum -= compactlu[i][k] * compactlu[k][j]
compactlu[i][j] = sum
dum = vv[i] * abs(sum)
if dum > big:
big = dum
imax = i
if j != imax:
# Substitute row imax and row j
imaxdum = permlist[imax] # NB in !!!!!!!!!!!!!!!!
jdum = permlist[j] # NB in !!!!!!!!!!!!!!!!
permlist[j] = imaxdum # NB in !!!!!!!!!!!!!!!!
permlist[imax] = jdum # NB in !!!!!!!!!!!!!!!!
for k in range(0, ndim):
dum = compactlu[imax][k]
compactlu[imax][k] = compactlu[j][k]
compactlu[j][k] = dum
parity = -parity
vv[imax] = vv[j]
#permlist[j] = imax # NB out !!!!!!!!!!!!!!!!!!!!!
divisor = float(compactlu[j][j])
if abs(divisor) < TINY: divisor = fsign(divisor) * TINY
dum = 1.0 / divisor
if j != ndm1:
jp1 = j + 1
for i in range(jp1, ndim):
compactlu[i][j] *= dum
lower = Matrix()
lower.zero(ndim, ndim)
upper = Matrix()
upper.zero(ndim, ndim)
for i in range(0, ndim):
for j in range(i, ndim):
lower[j][i] = compactlu[j][i]
for i in range(0, ndim):
lower[i][i] = 1.0
for i in range(0, ndim):
for j in range(i, ndim):
upper[i][j] = compactlu[i][j]
del compactlu
return lower, upper, permlist, parity
def lhs_sample(self, nparams, nintervals, rcorrmatrix=None, checklevel=0):
"""
Generates a full Latin Hypercube Sample of uniformly distributed
random variates in [0.0, 1.0] placed in a matrix with one realization
in each row. A target rank correlation matrix can be given (must have
the dimension nsamples*nsamples).
checklevel may be 0, 1 or 2 and is used to control trace printout.
0 produces no trace output, whereas 2 produces the most.
NB. IN ORDER FOR LATIN HYPERCUBE SAMPLING TO BE MEANINGFUL THE OUTPUT
STREAM OF RANDOM VARIATES MUST BE HANDLED BY INVERSE METHODS !!!!
Latin Hypercube Sampling was first described by McKay, Conover &
Beckman in a Technometrics article 1979. The use of the LHS technique
to introduce rank correlations was first described by Iman & Conover
1982 in an issue of Communications of Statistics.
"""
# lhs_sample uses the Matrix class to a great extent
if nparams > nintervals:
warn("nparams > nintervals in RandomStructure.lhs_sample")
nsamples = nintervals # Just to remember
rstreaminner = self.rstream
rstreamouter = self.rstream2
factor = 1.0 / float(nintervals)
tlhsmatrix1 = Matrix() # tlhsmatrix1 belongs to the Matrix class
if rcorrmatrix: tscorematrix = Matrix()
for k in range(0, nparams):
if rcorrmatrix:
tnvector, tscorevector = \
self.scramble_range(nsamples, rstreamouter, True)
rowk = array('d', tscorevector)
tscorematrix.append(rowk)
else:
tnvector = self.scramble_range(nsamples, rstreamouter)
pvector = array('d', [])
for number in tnvector:
p = factor * (float(number) + rstreaminner.runif01())
p = max(p, 0.0) # Probabilities must be in [0.0, 1.0]
p = min(p, 1.0)
pvector.append(p)
tlhsmatrix1.append(pvector)
# tlhsmatrix1 (and tscorematrix) are now transposed to run with
# one subsample per row to fit with output as well as Iman-Conover
# formulation. tlhsmatrix1 and tscorematrix will be used anyway
# for some manipulations which are more simple when matrices run
# with one variable per row
lhsmatrix1 = transposed(tlhsmatrix1)
if rcorrmatrix: scorematrix = transposed(tscorematrix)
if checklevel == 2:
print("lhs_sample: Original LHS sample matrix")
mxdisplay(lhsmatrix1)
if rcorrmatrix:
print("lhs_sample: Target rank correlation matrix")
mxdisplay(rcorrmatrix)
if checklevel == 1 or checklevel == 2:
print("lhs_sample: Rank correlation matrix of")
print(" original LHS sample matrix")
trankmatrix1 = Matrix()
for k in range(0, nparams):
rowk = array('d', extract_ranks(tlhsmatrix1[k]))
trankmatrix1.append(rowk)
mxdisplay(Matrix(corrmatrix(trankmatrix1)))
if not rcorrmatrix:
return lhsmatrix1
else:
scorecorr = Matrix(corrmatrix(tscorematrix))
if checklevel == 2:
print("lhs_sample: Score matrix of original LHS sample matrix")
mxdisplay(scorematrix)
print("lhs_sample: Correlation matrix of scores of")
print(" original LHS sample")
mxdisplay(scorecorr)
slower, slowert = ludcmp_chol(scorecorr)
slowerinverse = inverted(slower)
tslowerinverse = transposed(slowerinverse)
clower, clowert = ludcmp_chol(rcorrmatrix)
scoresnostar = scorematrix * tslowerinverse # Matrix multiplication
if checklevel == 2:
print("lhs_sample: Correlation matrix of scoresnostar")
mxdisplay(corrmatrix(transposed(scoresnostar)))
scoresstar = scoresnostar * clowert # Matrix multiplication
tscoresstar = transposed(scoresstar)
trankmatrix = Matrix()
for k in range(0, nparams):
trankmatrix.append(extract_ranks(tscoresstar[k]))
if checklevel == 2:
print("lhs_sample: scoresstar matrix")
mxdisplay(scoresstar)
print("lhs_sample: Correlation matrix of scoresstar")
mxdisplay(corrmatrix(tscoresstar))
print("lhs_sample: scoresstar matrix converted to rank")
mxdisplay(transposed(trankmatrix))
for k in range(0, nparams):
tlhsmatrix1[k] = array('d', sorted(list(tlhsmatrix1[k])))
print("RandomStructure.lhs_sample: Sorted LHS sample matrix")
mxdisplay(transposed(tlhsmatrix1))
tlhsmatrix2 = Matrix()
for k in range(0, nparams):
# Sort each row in tlhsmatrix1 and reorder
# according to trankmatrix rows
auxvec = reorder(tlhsmatrix1[k], trankmatrix[k], \
straighten=True)
tlhsmatrix2.append(auxvec)
lhsmatrix2 = transposed(tlhsmatrix2)
if checklevel == 2:
print("lhs_sample: Corrected/reordered LHS sample matrix")
mxdisplay(transposed(tlhsmatrix2))
if checklevel == 1 or checklevel == 2:
trankmatrix2 = Matrix()
auxmatrix2 = tlhsmatrix2
for k in range(0, nparams):
trankmatrix2.append(extract_ranks(auxmatrix2[k]))
print("lhs_sample: Rank correlation matrix of corrected/")
print(" /reordered LHS sample matrix")
mxdisplay(corrmatrix(trankmatrix2))
return lhsmatrix2
def ludcmp_crout_piv(matrix):
"""
Decomposes/factorizes square input matrix into a lower
and an upper matrix using Crout's algorithm WITH pivoting.
NB. It only works on square matrices!!!
"""
ndim = squaredim(matrix, 'ludcmp_crout_piv')
ndm1 = ndim - 1
vv = array('d', ndim*[0.0])
permlist = list(range(0, ndim))
parity = 1.0
imax = 0
# Copy to matrix to be processed (maintains the original matrix intact)
compactlu = deepcopy(matrix)
for i in range(0, ndim): # Copy and do some other stuff
big = 0.0
for j in range(0, ndim):
temp = abs(compactlu[i][j])
if temp > big: big = temp
assert big > 0.0
vv[i] = 1.0/big
# Perform the necessary manipulations:
for j in range(0, ndim):
for i in range(0, j):
sum = compactlu[i][j]
for k in range(0, i): sum -= compactlu[i][k] * compactlu[k][j]
compactlu[i][j] = sum
big = 0.0
for i in range(j, ndim):
sum = compactlu[i][j]
for k in range(0, j): sum -= compactlu[i][k] * compactlu[k][j]
compactlu[i][j] = sum
dum = vv[i] * abs(sum)
if dum > big:
big = dum
imax = i
if j != imax:
# Substitute row imax and row j
imaxdum = permlist[imax] # NB in !!!!!!!!!!!!!!!!
jdum = permlist[j] # NB in !!!!!!!!!!!!!!!!
permlist[j] = imaxdum # NB in !!!!!!!!!!!!!!!!
permlist[imax] = jdum # NB in !!!!!!!!!!!!!!!!
for k in range(0, ndim):
dum = compactlu[imax][k]
compactlu[imax][k] = compactlu[j][k]
compactlu[j][k] = dum
parity = - parity
vv[imax] = vv[j]
#permlist[j] = imax # NB out !!!!!!!!!!!!!!!!!!!!!
divisor = float(compactlu[j][j])
if abs(divisor) < TINY: divisor = fsign(divisor)*TINY
dum = 1.0 / divisor
if j != ndm1:
jp1 = j + 1
for i in range(jp1, ndim): compactlu[i][j] *= dum
lower = Matrix()
lower.zero(ndim, ndim)
upper = Matrix()
upper.zero(ndim, ndim)
for i in range(0, ndim):
for j in range(i, ndim): lower[j][i] = compactlu[j][i]
for i in range(0, ndim):
lower[i][i] = 1.0
for i in range(0, ndim):
for j in range(i, ndim): upper[i][j] = compactlu[i][j]
del compactlu
return lower, upper, permlist, parity
def nelder_mead(objfunc, point0, spans, \
trace=False, tolf=SQRTMACHEPS, tola=SQRTTINY, maxniter=256, \
rho=1.0, xsi=2.0, gamma=0.5, sigma=0.5):
"""
The Nelder & Mead downhill simplex method is designed to find the minimum
of an objective function that has a multi-dimensional input, (see for
instance Lagarias et al. (1998), "Convergence Properties of the Nelder-Mead
Simplex in Low Dimensions", SIAM J. Optim., Society for Industrial and
Applied Mathematics Vol. 9, No. 1, pp. 112-147 for details). The algorithm
is said to first have been presented by Nelder and Mead in Computer Journal,
Vol. 7, pp. 308-313 (1965).
The initial simplex must be entered by entering an initial point (an
array of coordinates), plus an array of spans for the corresponding
point coordinates.
For trace=True a trace is printed to stdout consisting of the present
number of iterations, the present low value of the objective function,
the present value of the absolute value of difference between the high and
the low value of the objective function, and the present list of vertices
of the low value of the objective function = the present "best" point.
tolf is the fractional tolerance and tola is the absolute tolerance of
the absolute value of difference between the high and the low value of
the objective function.
maxniter is the maximum allowed number of iterations.
rho, xsi, gamma and sigma are the parameters for reflection, expansion,
contraction and shrinkage, respectively (cf. the references above).
"""
# Check the input parameters
assert is_nonneginteger(maxniter), \
"max number of iterations must be a non-negative integer in nelder_mead!"
if tolf < MACHEPS:
tolf = MACHEPS
wtext = "fractional tolerance smaller than machine epsilon is not "
wtext += "recommended in nelder_mead. Machine epsilon is used instead"
warn(wtext)
assert rho > 0.0, "rho must be positive in nelder_mead!"
assert xsi > 1.0, "xsi must be > 1.0 in nelder_mead!"
assert xsi > rho, "xsi must be > rho in nelder_mead!"
assert 0.0 < gamma < 1.0, "gamma must be in (0.0, 1.0) in nelder_mead!"
assert 0.0 < sigma < 1.0, "sigma be in (0.0, 1.0) in nelder_mead!"
assert tola >= 0.0, "absolute tolerance must be positive in nelder_mead!"
# Prepare matrix of vertices
ndim = len(point0)
assert len(spans) == ndim
vertices = Matrix()
vertices.append(array('d', list(point0)))
ndimp1 = ndim + 1
fndim = float(ndim)
for j in range(0, ndim): vertices.append(array('d', list(point0)))
for j in range(0, ndim): vertices[j+1][j] += spans[j]
# Prepare a few variants of parameters
oneprho = 1.0 + rho
# LOOP!!!!!!!!
niter = 0
while True:
niter += 1
if niter > maxniter:
txt1 = "nelder_mead did not converge. Absolute error = "
txt2 = str(abs(high-low)) + " for " + str(niter-1)
txt3 = " iterations. Consider new tols or maxniter!"
raise Error(txt1+txt2+txt3)
# Compute the objective function values for the vertices
flist = array('d', [])
for k in range(0, ndimp1):
fk = objfunc(vertices[k])
flist.append(fk)
# Establish the highest point, the next highest point and the lowest
low = flist[0]
high = nxhi = low
ilow = 0
ihigh = 0
for k in range(1, ndimp1):
fk = flist[k]
if fk > high:
nxhi = high
high = fk
ihigh = k
elif fk < low:
low = fk
ilow = k
if trace: print(niter, low, abs(high-low), list(vertices[ilow]))
if low < tola: tol = tola
else: tol = abs(low)*tolf
if abs(high-low) < tol: return low, list(vertices[ilow])
# Reflect the high point
# First find a new vertix = the centroid of the non-max vertices
cntr = array('d', ndim*[float('nan')])
newr = array('d', ndim*[float('nan')])
for j in range(0, ndim):
xsum = 0.0
for k in range(0, ndimp1):
if k != ihigh:
xsum += vertices[k][j]
cntr[j] = xsum/fndim
# Then move from the centroid in an away-from-max direction
for j in range(0, ndim):
newr[j] = oneprho*cntr[j] - rho*vertices[ihigh][j]
# Check the new vertix
accepted = False
phir = objfunc(newr)
if low <= phir < nxhi:
# Everything is OK!
if trace: print("Reflection sufficient")
vertices[ihigh] = newr
phi = phir
accepted = True
elif phir < low:
# Expand:
if trace: print("Expansion")
newe = array('d', ndim*[float('nan')])
for j in range(0, ndim):
newe[j] = cntr[j] + xsi*(newr[j]-cntr[j])
phie = objfunc(newe)
if phie < phir:
vertices[ihigh] = newe
phi = phie
else:
vertices[ihigh] = newr
phi = phir
accepted = True
elif phir >= nxhi:
# Contract
if phir < high:
# -outside:
if trace: print("Outside contraction")
newo = array('d', ndim*[float('nan')])
for j in range(0, ndim):
newo[j] = cntr[j] + gamma*(newr[j]-cntr[j])
phio = objfunc(newo)
if phio <= phir:
vertices[ihigh] = newo
phi = phio
accepted = True
else:
# -inside:
if trace: print("Inside contraction")
newi = array('d', ndim*[float('nan')])
for j in range(0, ndim):
newi[j] = cntr[j] - gamma*(cntr[j]-vertices[ihigh][j])
phii = objfunc(newi)
if phii <= high:
vertices[ihigh] = newi
phi = phii
accepted = True
if not accepted:
# Shrink:
if trace: print("Shrinkage")
for k in range(0, ndimp1):
for j in range(j, ndim):
vertices[k][j] = vertices[ilow][j] + sigma*(vertices[k][j] -
vertices[ilow][j])
# end of nelder_mead
# ------------------------------------------------------------------------------
def lhs_sample(self, nparams, nintervals, rcorrmatrix=None, checklevel=0):
"""
Generates a full Latin Hypercube Sample of uniformly distributed
random variates in [0.0, 1.0] placed in a matrix with one realization
in each row. A target rank correlation matrix can be given (must have
the dimension nsamples*nsamples).
checklevel may be 0, 1 or 2 and is used to control trace printout.
0 produces no trace output, whereas 2 produces the most.
NB. IN ORDER FOR LATIN HYPERCUBE SAMPLING TO BE MEANINGFUL THE OUTPUT
STREAM OF RANDOM VARIATES MUST BE HANDLED BY INVERSE METHODS !!!!
Latin Hypercube Sampling was first described by McKay, Conover &
Beckman in a Technometrics article 1979. The use of the LHS technique
to introduce rank correlations was first described by Iman & Conover
1982 in an issue of Communications of Statistics.
"""
# lhs_sample uses the Matrix class to a great extent
if nparams > nintervals:
warn("nparams > nintervals in RandomStructure.lhs_sample")
nsamples = nintervals # Just to remember
rstreaminner = self.rstream
rstreamouter = self.rstream2
factor = 1.0 / float(nintervals)
tlhsmatrix1 = Matrix() # tlhsmatrix1 belongs to the Matrix class
if rcorrmatrix: tscorematrix = Matrix()
for k in range(0, nparams):
if rcorrmatrix:
tnvector, tscorevector = \
self.scramble_range(nsamples, rstreamouter, True)
rowk = array('d', tscorevector)
tscorematrix.append(rowk)
else:
tnvector = self.scramble_range(nsamples, rstreamouter)
pvector = array('d', [])
for number in tnvector:
p = factor * (float(number) + rstreaminner.runif01())
p = max(p, 0.0) # Probabilities must be in [0.0, 1.0]
p = min(p, 1.0)
pvector.append(p)
tlhsmatrix1.append(pvector)
# tlhsmatrix1 (and tscorematrix) are now transposed to run with
# one subsample per row to fit with output as well as Iman-Conover
# formulation. tlhsmatrix1 and tscorematrix will be used anyway
# for some manipulations which are more simple when matrices run
# with one variable per row
lhsmatrix1 = transposed(tlhsmatrix1)
if rcorrmatrix: scorematrix = transposed(tscorematrix)
if checklevel == 2:
print("lhs_sample: Original LHS sample matrix")
mxdisplay(lhsmatrix1)
if rcorrmatrix:
print("lhs_sample: Target rank correlation matrix")
mxdisplay(rcorrmatrix)
if checklevel == 1 or checklevel == 2:
print("lhs_sample: Rank correlation matrix of")
print(" original LHS sample matrix")
trankmatrix1 = Matrix()
for k in range (0, nparams):
rowk = array('d', extract_ranks(tlhsmatrix1[k]))
trankmatrix1.append(rowk)
mxdisplay(Matrix(corrmatrix(trankmatrix1)))
if not rcorrmatrix:
return lhsmatrix1
else:
scorecorr = Matrix(corrmatrix(tscorematrix))
if checklevel == 2:
print("lhs_sample: Score matrix of original LHS sample matrix")
mxdisplay(scorematrix)
print("lhs_sample: Correlation matrix of scores of")
print(" original LHS sample")
mxdisplay(scorecorr)
slower, slowert = ludcmp_chol(scorecorr)
slowerinverse = inverted(slower)
tslowerinverse = transposed(slowerinverse)
clower, clowert = ludcmp_chol(rcorrmatrix)
scoresnostar = scorematrix*tslowerinverse # Matrix multiplication
if checklevel == 2:
print("lhs_sample: Correlation matrix of scoresnostar")
mxdisplay(corrmatrix(transposed(scoresnostar)))
scoresstar = scoresnostar*clowert # Matrix multiplication
tscoresstar = transposed(scoresstar)
trankmatrix = Matrix()
for k in range (0, nparams):
trankmatrix.append(extract_ranks(tscoresstar[k]))
if checklevel == 2:
print("lhs_sample: scoresstar matrix")
mxdisplay(scoresstar)
print("lhs_sample: Correlation matrix of scoresstar")
mxdisplay(corrmatrix(tscoresstar))
print("lhs_sample: scoresstar matrix converted to rank")
mxdisplay(transposed(trankmatrix))
for k in range(0, nparams):
tlhsmatrix1[k] = array('d', sorted(list(tlhsmatrix1[k])))
print("RandomStructure.lhs_sample: Sorted LHS sample matrix")
mxdisplay(transposed(tlhsmatrix1))
tlhsmatrix2 = Matrix()
for k in range(0, nparams):
# Sort each row in tlhsmatrix1 and reorder
# according to trankmatrix rows
auxvec = reorder(tlhsmatrix1[k], trankmatrix[k], \
straighten=True)
tlhsmatrix2.append(auxvec)
lhsmatrix2 = transposed(tlhsmatrix2)
if checklevel == 2:
print("lhs_sample: Corrected/reordered LHS sample matrix")
mxdisplay(transposed(tlhsmatrix2))
if checklevel == 1 or checklevel == 2:
trankmatrix2 = Matrix()
auxmatrix2 = tlhsmatrix2
for k in range (0, nparams):
trankmatrix2.append(extract_ranks(auxmatrix2[k]))
print("lhs_sample: Rank correlation matrix of corrected/")
print(" /reordered LHS sample matrix")
mxdisplay(corrmatrix(trankmatrix2))
return lhsmatrix2