def optimize_openopt(self, solver='interalg'):
if not have_openopt:
raise RuntimeError('OpenOpt not available.')
p = GLP(self.get_cost_function,
self.par.get_array(),
lb=self.par.get_lower_bounds(),
ub=self.par.get_upper_bounds())
r = p.solve(solver)
print(r, file=log)
self.set_parameters_from_array(r.xf)
print('=== OPTIMIZED PARAMETER SET ===', file=log)
self.get_cost_function(r.xf)
return self.par
# define objective
f = (x-1.5)**2 + sin(0.8 * y ** 2 + 15)**4 + cos(0.8 * z ** 2 + 15)**4 + (t-7.5)**4
# define some constraints
constraints = [x<1, x>-1, y<1, y>-1, z<1, z>-1, t<1, t>-1, x+2*y>-1.5, sinh(x)+cosh(z)+sinh(t) <2.0]
# add some more constraints via Python "for" cycle
M = 10
for i in range(M):
func = i*x+(M-i)*y+sinh(z)+cosh(t)
constraints.append(func < i+1)
# define start point. You can use variables with length > 1 as well
startPoint = {x:0, y:0, z:0, t:0}
# assign prob
p = GLP(f, startPoint, constraints=constraints, maxIter = 1e3, maxFunEvals = 1e5, maxTime = 5, maxCPUTime = 5)
#optional: graphic output
#p.plot = 1 or p.solve(..., plot=1) or p = GLP(..., plot=1)
# solve
r = p.solve('de', plot=1) # try other solvers: galileo, pswarm
optPoint, optVal = r.xf, r.ff
x, y, z, t = optPoint[x], optPoint[y], optPoint[z], optPoint[t]
# or
# x, y, z, t = x(optPoint), y(optPoint), z(optPoint), t(optPoint)
theta = [0.2, 0.2]
# y = copy.copy(solution[:,1:2])
# y[1::] = y[1::] + numpy.random.normal(loc=0.0,scale=0.1,size=numStep-1)
# odeSIR = odeLossFunc.squareLoss([0.5,1.0/3.0] ,ode,x0,t0,t[1:len(t)],y[1:len(t)],'R')
objSIR = odeLossFunc.squareLoss(theta, ode, x0, t0, t[1::], solution[1::, 1:3],
['I', 'R'])
box = [(0., 2.), (0., 2.)]
npBox = numpy.array(box)
lb = npBox[:, 0]
ub = npBox[:, 1]
pro = GLP(f=objSIR.cost, x0=theta, lb=lb, ub=ub)
pro.plot = True
rGalileo = pro.solve('galileo')
pro = GLP(f=objSIR.cost, x0=theta, lb=lb, ub=ub)
pro.plot = True
rDe = pro.solve('de')
pro = GLP(f=objSIR.cost, x0=theta, lb=lb, ub=ub)
pro.plot = True
rPSwarm = pro.solve('pswarm')
pro = NLP(f=objSIR.cost, df=objSIR.sensitivity, x0=theta, lb=lb, ub=ub)
pro.plot = True
rLincher = pro.solve('lincher')
json.dump(best, fresults)
fresults.close()
if DB:
try:
DB.results.insert(
{
"score": best[0],
"date": datetime.datetime.now(),
"params": vars[beta],
"range": rng,
"beta": beta,
"tested_vars": var_names,
}
)
except Exception, e:
print "MONGO INSERT ERROR:%s" % e
return ret
p = GLP(getscore, x0=startPoint, lb=lbs, ub=ubs, maxIter=100, maxFunEvals=10000)
p.fOpt = 170000 # Optimal value we could have
r = p.maximize("de", iprint=1, plot=0) # , searchDirectionStrategy="best")
# r = p.maximize('galileo', iprint=1, plot=0, population=5)
# r = p.maximize('gsubg', iprint=1, plot=0)
print "Solution vector: %s" % p.xf
print "Max value: %s" % p.ff
from openopt import GLP
from numpy import *
f = lambda x: (x[0]-1.5)**2 + sin(0.8 * x[1] ** 2 + 15)**4 + cos(0.8 * x[2] ** 2 + 15)**4 + (x[3]-7.5)**4
p = GLP(f, lb = -ones(4), ub = ones(4), maxIter = 1e3, maxFunEvals = 1e5, maxTime = 3, maxCPUTime = 3)
#optional: graphic output
#p.plot = 1 or p.solve(..., plot=1) or p = GLP(..., plot=1)
r = p.solve('de', plot=1)
x_opt, f_opt = r.xf, r.ff
from openopt import GLP
from numpy import *
f = lambda x: (x[0] - 1.5)**2 + sin(0.8 * x[1]**2 + 15)**4 + cos(0.8 * x[
2]**2 + 15)**4 + (x[3] - 7.5)**4
p = GLP(f,
lb=-ones(4),
ub=ones(4),
maxIter=1e3,
maxFunEvals=1e5,
maxTime=3,
maxCPUTime=3)
#optional: graphic output
#p.plot = 1
r = p.solve('pswarm', x0=[0, 0, 0, 0], plot=0, debug=1, maxIter=200)
x_opt, f_opt = r.xf, r.ff
from openopt import GLP
from numpy import *
f = lambda x: (x * x - 10 * cos(2 * pi * x) + 10).sum() #Rastrigin function
p = GLP(f,
lb=-ones(10) * 5.12,
ub=ones(10) * 5.12,
maxIter=1e3,
maxFunEvals=1e5,
maxTime=10,
maxCPUTime=10)
r = p.solve('de', plot=0)
x_opt, f_opt = r.xf, r.ff
print x_opt
constraints = [
P(a**2 - z + b * c < 4.7) <
0.03, # by default constraint tolerance is 10^-6
(P(c / b + z > sin(x)) > 0.02)(
tol=1e-10
), # use tol 10^-10 instead; especially useful for equality constraints
mean(b + y) <= 3.5
]
startPoint = {x: 0, y: 0, z: 0, a: A, b: B, c: C}
''' This is multiextremum problem (due to sin, cos etc),
thus we have to use global nonlinear solver capable of handling nonlinear constraints
(BTW having probability functions P() make it even discontinuous for discrete distribution(s) involved)
'''
p = GLP(objective, startPoint, constraints=constraints)
solver = 'de' # named after "differential evolution", check http://openopt.org/GLP for other available global solvers
r = p.maximize(solver, maxTime=150, maxDistributionSize=100, iprint=50)
'''
------------------------- OpenOpt 0.45 -------------------------
solver: de problem: unnamed type: GLP
iter objFunVal log10(MaxResidual/ConTol)
0 6.008e+00 8.40
50 7.436e+00 -100.00
93 7.517e+00 -100.00
istop: 11 (Non-Success Number > maxNonSuccess = 15)
Solver: Time Elapsed = 31.58 CPU Time Elapsed = 30.07
objFunValue: 7.516546 (feasible, max(residuals/requiredTolerances) = 0)
'''
print(r(x, y,
z)) # [0.99771171590186, -0.15952854483416395, 0.8584877921129496]
from openopt import GLP
from numpy import *
f = lambda x: (x[0] - 1.5) ** 2 + sin(0.8 * x[1] ** 2 + 15) ** 4 + cos(0.8 * x[2] ** 2 + 15) ** 4 + (x[3] - 7.5) ** 4
p = GLP(f, lb=-ones(4), ub=ones(4), maxIter=1e3, maxFunEvals=1e5, maxTime=3, maxCPUTime=3)
# optional: graphic output
# p.plot = 1 or p.solve(..., plot=1) or p = GLP(..., plot=1)
r = p.solve("de", plot=1)
x_opt, f_opt = r.xf, r.ff
from openopt import GLP
from numpy import *
N = 100
aN = arange(N)
f = lambda x: ((x - aN)**2).sum()
p = GLP(f,
lb=-ones(N),
ub=N * ones(N),
maxIter=1e3,
maxFunEvals=1e5,
maxTime=10,
maxCPUTime=300)
#optional: graphic output
#p.plot = 1
r = p.solve('de', plot=1, debug=1, iprint=0)
x_opt, f_opt = r.xf, r.ff
from openopt import GLP
from numpy import *
# objective function
# (x0 - 1.5)^2 + sin(0.8 * x1^2 + 15)^4 + cos(0.8 * x2^2 + 15)^4 + (x3 - 7.5)^4 -> min
f = lambda x: (x[0]-1.5)**2 + sin(0.8 * x[1] ** 2 + 15)**4 + cos(0.8 * x[2] ** 2 + 15)**4 + (x[3]-7.5)**4
# box-bound constraints lb <= x <= ub
lb, ub = -ones(4), ones(4)
# linear inequality constraints
# x0 + x3 <= 0.15
# x1 + x3 <= 1.5
# as Ax <= b
A = mat('1 0 0 1; 0 1 0 1') # tuple, list, numpy array etc are OK as well
b = [0.15, 1.5] # tuple, list, numpy array etc are OK as well
# non-linear constraints
# x0^2 + x2^2 <= 0.15
# 1.5 * x0^2 + x1^2 <= 1.5
c = lambda x: (x[0] ** 2 + x[2] ** 2 - 0.15, 1.5 * x[0] ** 2 + x[1] ** 2 - 1.5)
p = GLP(f, lb=lb, ub=ub, A=A, b=b, c=c, maxIter = 250, maxFunEvals = 1e5, maxTime = 30, maxCPUTime = 30)
r = p.solve('de', mutationRate = 0.15, plot=1)
x_opt, f_opt = r.xf, r.ff
# print(L_T_tilde(theta_tilde))
# res = minimize(L_T_tilde, theta_tilde, method = 'COBYLA', constraints = constraints)
# print(res)
# assert isfinite(res.fun)
# theta_tilde = res.x
# print('p', [p(theta_tilde, i) for i in k_underline])
# print('alpha', [alpha(theta_tilde, i) for i in k_underline])
# print('beta', [beta(theta_tilde, i) for i in k_underline])
# # NLopt
# theta_tilde = opt.optimize(theta_tilde)
# L_T_tilde_ast = opt.last_optimum_value()
# print(L_T_tilde_ast)
# result = opt.last_optimize_result()
# print(result)
# OpenOpt
opt_p = GLP(L_T_tilde, theta_tilde, df = grad_L_T_tilde, A = opt_A, b = opt_b, lb = opt_lb, ub = opt_ub)
res = opt_p.solve('de', maxNonSuccess = 32) # maxNonSuccess = round(exp(len(theta_tilde)))
print(res.xf, res.ff)
# print('Basin-Hopping')
# print(L_T_tildeconstrained(theta_tilde))
# res = basinhopping(L_T_tildeconstrained, theta_tilde)
# print(res)
# assert isfinite(res.fun)
# theta_tilde = res.x
# print('p', [p(theta_tilde, i) for i in k_underline])
# print('alpha', [alpha(theta_tilde, i) for i in k_underline])
# print('beta', [beta(theta_tilde, i) for i in k_underline])
def fittingOpenopt(pearr, tmatrix, minR, maxR, lbounds, ubounds, gmaxtime,
pfact, res):
nrgauss = int((len(lbounds) + 1) / 3)
rvecbins = tmatrix.getMatrix().shape[0]
myrange = maxR - minR
xarr = numpy.linspace(minR + myrange / rvecbins / 2,
maxR - myrange / rvecbins / 2, rvecbins)
xxarr = numpy.array([xarr] * nrgauss)
if pfact == 0:
print "Will not apply a penalty for gaussian proximity."
minfuncwrap = lambda x: gaussSQDiff(x, tmatrix.getMatrix(), pearr,
xxarr)
else:
print "Will penalize gaussians which are closer than %d times the sum of both sigmas."
minfuncwrap = lambda x: penalizeCloseGauss(x, tmatrix.getMatrix(),
pearr, xxarr, pfact)
lines_distance, lines_efficiency, g_lines, chsql, chisqs, chisqax = createLivePlot(
nrgauss, pearr, tmatrix, xarr, lbounds, ubounds)
mycallback = lambda p: plotCallback(p, lines_distance, lines_efficiency,
g_lines, xxarr, tmatrix, chsql, chisqs,
chisqax)
print "Starting openopt ##########################"
prob = GLP(minfuncwrap,
lb=lbounds,
ub=ubounds,
callback=mycallback,
maxFunEvals=1e15,
maxNonSuccess=200,
maxIter=1e5,
maxTime=gmaxtime,
fEnough=res)
result = prob.solve('de', population=1000 * len(lbounds))
# result=prob.solve('asa')
# result=prob.solve('galileo') # not good
# result=prob.solve('pswarm')
# prob = GLP(minfuncwrap,lb=lbounds,ub=ubounds,callback=mycallback,maxNonSuccess=200,maxIter=1e5,maxTime=gmaxtime)
# result=prob.solve('isres',population=100*len(lbounds))
# prob = NLP(minfuncwrap,lb=lbounds,ub=ubounds,callback=mycallback,maxNonSuccess=200,maxIter=1e5,maxTime=gmaxtime)
# result=prob.solve('scipy_lbfgsb')
# result=prob.solve('scipy_tnc')
# result=prob.solve('bobyqa')
# result=prob.solve('ptn')
# result=prob.solve('slmvm1')
# result=prob.solve('slmvm2')
# result=prob.solve('ralg')
# result=prob.solve('scipy_cobyla') #good!!
# result=prob.solve('mma')
# result=prob.solve('auglag')
# result=prob.solve('gsubg')
xopt = result.xf
# prob2 = prob = NLP(minfuncwrap, xopt , lb = lbounds, ub = ubounds, callback = mycallback, maxNonSuccess = 20, maxIter = 1e5, maxTime = gmaxtime)
# result = prob2.solve('scipy_cobyla')
# xopt = result.xf
print "Minimum function chisq", result.ff
nrgauss, a_final, r_final, sig_final = x2parms(xopt)
print "G\tA\t\tx0\t\tsigma"
nr = 1
for a, r, sig in zip(a_final, r_final, sig_final):
print "%d\t%f\t%f\t%f\t" % (nr, a, r, sig)
nr += 1
gaussians = (a_final * numpy.exp(-(xxarr.T - r_final)**2 /
(2.0 * sig_final**2)))
r_prdist = gaussians.sum(axis=1)
e_fitprdist = numpy.dot(r_prdist, tmatrix.getMatrix())
r_prdist /= r_prdist.sum()
e_fitprdist /= e_fitprdist.sum()
return r_prdist, xarr, e_fitprdist, (a_final, r_final, sig_final)
# latter (using p.scale) is more recommended
# because it affects xtol for those solvers
# who use OO stop criteria
# (ralg, lincher, nsmm, nssolve and mb some others)
# xtol will be compared to scaled x shift:
# is || (x[k] - x[k-1]) * scale || < xtol
# You can define scale and diffInt as
# numpy arrays, matrices, Python lists, tuples
p = NLP(f, x0, c=c, scale=[1, coeff], **someModifiedStopCriteria)
r = p.solve('ipopt')
print(
r.ff, r.xf
) # "24.999996490694787 [ 1.50000004e+01 8.00004473e+09]" - much better
"""
GLP (GLobal Problem from OpenOpt set) example for FuncDesigner model:
searching for global minimum of the func
(x-1.5)**2 + sin(0.8 * y ** 2 + 15)**4 + cos(0.8 * z ** 2 + 15)**4 + (t-7.5)**4
subjected to some constraints
See http://openopt.org/GLP for more info and examples.
"""
from openopt import GLP
from FuncDesigner import *
x, y, z, t = oovars(4)
# define objective
f = (x - 1.5)**2 + sin(0.8 * y**2 + 15)**4 + cos(0.8 * z**2 + 15)**4 + (t -
7.5)**4
from openopt import GLP
from numpy import *
f = lambda x: (x[0]-1.5)**2 + sin(0.8 * x[1] ** 2 + 15)**4 + cos(0.8 * x[2] ** 2 + 15)**4 + (x[3]-7.5)**4
p = GLP(f, lb = -ones(4), ub = ones(4), maxIter = 1e3, maxFunEvals = 1e5, maxTime = 3, maxCPUTime = 3)
#optional: graphic output
#p.plot = 1
r = p.solve('pswarm', x0=[0, 0, 0, 0], plot=0, debug=1, maxIter=200)
x_opt, f_opt = r.xf, r.ff
b=b)
pro.plot = True
rSLSQP = pro.solve('ralg')
pro = NLP(f=objLegrand.cost,
x0=rPswarm.xf,
df=objLegrand.sensitivity,
lb=lb,
ub=ub,
A=A,
b=b)
pro.plot = True
rSLSQP = pro.solve('scipy_slsqp')
# GLP
pro = GLP(f=objLegrand.cost, x0=theta, df=objLegrand.sensitivity, lb=lb, ub=ub)
pro.plot = True
rPswarm = pro.solve('pswarm')
pro2 = GLP(f=objLegrand.cost,
x0=rPswarm.xf,
df=objLegrand.sensitivity,
lb=lb,
ub=ub)
pro2.plot = True
rPswarm2 = pro2.solve('pswarm')
pro3 = NLP(f=objLegrand.cost,
x0=rPswarm2.xf,
df=objLegrand.sensitivity,
lb=lb,
pro.plot = True
rLincher = pro.solve('lincher')
pro = NLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro = NLP(f=objLegrand.cost,x0=resDE['x'],df=objLegrand.sensitivity,lb=lb,ub=ub)
pro.plot = True
rSLSQP = pro.solve('scipy_slsqp')
# GLP
pro = GLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro = GLP(f=objLegrand.cost,x0=resDE['x'],df=objLegrand.sensitivity,lb=lb,ub=ub)
pro.plot = True
rPswarm = pro.solve('pswarm',size=50,maxFunEvals=100000,maxIter=1000)
pro2 = GLP(f=objLegrand.cost,x0=rPswarm.xf,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro2.plot = True
rPswarm2 = pro2.solve('pswarm')
pro3 = NLP(f=objLegrand.cost,x0=rPswarm2.xf,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro3.plot = True
rPswarm3 = pro3.solve('ralg')
pro = GLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro.plot = True
rGalileo = pro.solve('galileo')
pro = GLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro.plot = True
rDe = pro.solve('de')
pro.plot = True
rSLSQP = pro.solve('ralg')
pro = NLP(f=objLegrand.cost,x0=rPswarm.xf,df=objLegrand.sensitivity,lb=lb,ub=ub,A=A,b=b)
pro.plot = True
rSLSQP = pro.solve('scipy_slsqp')
objLegrand.cost(rPswarm.xf)
objLegrand.cost()
gSens,output=objLegrand.sensitivity(full_output=True)
solution = output['sens'][:,:6]
# here we pretend the bounds don't exist
pro2 = GLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro2.plot = True
r2 = pro2.solve('galileo')
pro = GLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub,A=A,b=b)
pro.plot = True
rDe = pro.solve('de')
pro = GLP(f=objLegrand.cost,x0=theta,lb=lb,ub=ub,A=A,b=b)
pro.plot = True
rPswarm = pro.solve('pswarm',size=100)
pro = GLP(f=objLegrand.cost,x0=rPswarm.xf,lb=lb,ub=ub,A=A,b=b)
pro.plot = True
rPswarm = pro.solve('pswarm',size=100,maxIter=1000,maxFunEvals=100000)
from openopt import GLP
from numpy import *
f = lambda x: (x[0]-1.5)**2 + sin(0.8 * x[1] ** 2 + 15)**4 + cos(0.8 * x[2] ** 2 + 15)**4 + (x[3]-7.5)**4
p = GLP(f, lb = -ones(4), ub = ones(4), maxIter = 1e3, maxFunEvals = 1e5, maxTime = 3, maxCPUTime = 3)
#optional: graphic output
#p.plot = 1 or p.solve(..., plot=1) or p = GLP(..., plot=1)
r = p.solve('de', plot=1)
x_opt, f_opt = r.xf, r.ff
from openopt import GLP
from numpy import *
N = 100
aN = arange(N)
f = lambda x: ((x-aN)**2).sum()
p = GLP(f, lb = -ones(N), ub = N*ones(N), maxIter = 1e3, maxFunEvals = 1e5, maxTime = 10, maxCPUTime = 300)
#optional: graphic output
#p.plot = 1
r = p.solve('de', plot=1, debug=1, iprint=0)
x_opt, f_opt = r.xf, r.ff
"""
GLP (GLobal Problem from OpenOpt set) example for FuncDesigner model:
searching for global minimum of the func
(x-1.5)**2 + sin(0.8 * y ** 2 + 15)**4 + cos(0.8 * z ** 2 + 15)**4 + (t-7.5)**4
subjected to some constraints
See http://openopt.org/GLP for more info and examples.
"""
from openopt import GLP
from FuncDesigner import *
x, y, z, t = oovars(4)
# define objective
f = (x - 1.5)**2 + sin(0.8 * y**2 + 15)**4 + cos(0.8 * z**2 + 15)**4 + (t -
7.5)**4
# define some constraints
constraints = [
x < 1, x > -1, y < 1, y > -1, z < 1, z > -1, t < 1, t > -1,
x + 2 * y > -1.5,
sinh(x) + cosh(z) + sinh(t) < 2.0
]
# add some more constraints via Python "for" cycle
M = 10
for i in range(M):
func = i * x + (M - i) * y + sinh(z) + cosh(t)
constraints.append(func < i + 1)
# define start point. You can use variables with length > 1 as well
objective = 0.15 * mean(f + 2 * x) + x * cos(y + 2 * z) + z * var(b) * std(c) + y * P(a - z + b * sin(c) > 5)
constraints = [
P(a ** 2 - z + b * c < 4.7) < 0.03, # by default constraint tolerance is 10^-6
(P(c / b + z > sin(x)) > 0.02)(tol=1e-10), # use tol 10^-10 instead; especially useful for equality constraints
mean(b + y) <= 3.5,
]
startPoint = {x: 0, y: 0, z: 0, a: A, b: B, c: C}
""" This is multiextremum problem (due to sin, cos etc),
thus we have to use global nonlinear solver capable of handling nonlinear constraints
(BTW having probability functions P() make it even discontinuous for discrete distribution(s) involved)
"""
p = GLP(objective, startPoint, constraints=constraints)
solver = "de" # named after "differential evolution", check http://openopt.org/GLP for other available global solvers
r = p.maximize(solver, maxTime=150, maxDistributionSize=100)
""" output for Intel Atom 1.6 GHz (may differ due to random numbers involved in solver "de")
------------------------- OpenOpt 0.39 -------------------------
solver: de problem: unnamed type: GLP
iter objFunVal log10(MaxResidual/ConTol)
0 6.008e+00 8.40
10 6.638e+00 -100.00
20 7.318e+00 -100.00
30 7.423e+00 -100.00
40 7.475e+00 -100.00
50 7.490e+00 -100.00
53 7.490e+00 -100.00
istop: -9 (max time limit has been reached)
Solver: Time Elapsed = 150.34 CPU Time Elapsed = 145.24
pro = NLP(f=objLegrand.cost,x0=rPswarm.xf,df=objLegrand.sensitivity,lb=lb,ub=ub,A=A,b=b)
pro.plot = True
rSLSQP = pro.solve('ralg')
pro = NLP(f=objLegrand.cost,x0=rPswarm.xf,df=objLegrand.sensitivity,lb=lb,ub=ub,A=A,b=b)
pro.plot = True
rSLSQP = pro.solve('scipy_slsqp')
# GLP
pro = GLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro.plot = True
rPswarm = pro.solve('pswarm')
pro2 = GLP(f=objLegrand.cost,x0=rPswarm.xf,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro2.plot = True
rPswarm2 = pro2.solve('pswarm')
pro3 = NLP(f=objLegrand.cost,x0=rPswarm2.xf,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro3.plot = True
rPswarm3 = pro3.solve('ralg')
pro2 = GLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub)
pro2.plot = True
r2 = pro2.solve('galileo')
pro = GLP(f=objLegrand.cost,x0=theta,df=objLegrand.sensitivity,lb=lb,ub=ub,A=A,b=b)
pro.plot = True
rDe = pro.solve('de')
def fittingOpenopt(pearr, tmatrix, minR, maxR, lbounds, ubounds, gmaxtime, pfact, res):
nrgauss = int((len(lbounds) + 1) / 3)
rvecbins = tmatrix.getMatrix().shape[0]
myrange = maxR - minR
xarr = numpy.linspace(minR + myrange / rvecbins / 2, maxR - myrange / rvecbins / 2, rvecbins)
xxarr = numpy.array([xarr] * nrgauss)
if pfact == 0:
print "Will not apply a penalty for gaussian proximity."
minfuncwrap = lambda x: gaussSQDiff(x, tmatrix.getMatrix(), pearr, xxarr)
else:
print "Will penalize gaussians which are closer than %d times the sum of both sigmas."
minfuncwrap = lambda x: penalizeCloseGauss(x, tmatrix.getMatrix(), pearr, xxarr, pfact)
lines_distance, lines_efficiency, g_lines, chsql, chisqs, chisqax = createLivePlot(nrgauss, pearr, tmatrix, xarr, lbounds, ubounds)
mycallback = lambda p: plotCallback(p, lines_distance, lines_efficiency, g_lines, xxarr, tmatrix, chsql, chisqs, chisqax)
print "Starting openopt ##########################"
prob = GLP(minfuncwrap, lb = lbounds, ub = ubounds, callback = mycallback, maxFunEvals = 1e15, maxNonSuccess = 200, maxIter = 1e5, maxTime = gmaxtime, fEnough = res)
result = prob.solve('de', population = 1000 * len(lbounds))
# result=prob.solve('asa')
# result=prob.solve('galileo') # not good
# result=prob.solve('pswarm')
# prob = GLP(minfuncwrap,lb=lbounds,ub=ubounds,callback=mycallback,maxNonSuccess=200,maxIter=1e5,maxTime=gmaxtime)
# result=prob.solve('isres',population=100*len(lbounds))
# prob = NLP(minfuncwrap,lb=lbounds,ub=ubounds,callback=mycallback,maxNonSuccess=200,maxIter=1e5,maxTime=gmaxtime)
# result=prob.solve('scipy_lbfgsb')
# result=prob.solve('scipy_tnc')
# result=prob.solve('bobyqa')
# result=prob.solve('ptn')
# result=prob.solve('slmvm1')
# result=prob.solve('slmvm2')
# result=prob.solve('ralg')
# result=prob.solve('scipy_cobyla') #good!!
# result=prob.solve('mma')
# result=prob.solve('auglag')
# result=prob.solve('gsubg')
xopt = result.xf
# prob2 = prob = NLP(minfuncwrap, xopt , lb = lbounds, ub = ubounds, callback = mycallback, maxNonSuccess = 20, maxIter = 1e5, maxTime = gmaxtime)
# result = prob2.solve('scipy_cobyla')
# xopt = result.xf
print "Minimum function chisq", result.ff
nrgauss, a_final, r_final, sig_final = x2parms(xopt)
print "G\tA\t\tx0\t\tsigma"
nr = 1
for a, r, sig in zip(a_final, r_final, sig_final):
print "%d\t%f\t%f\t%f\t" % (nr, a, r, sig)
nr += 1
gaussians = (a_final * numpy.exp(-(xxarr.T - r_final) ** 2 / (2.0 * sig_final ** 2)))
r_prdist = gaussians.sum(axis = 1)
e_fitprdist = numpy.dot(r_prdist, tmatrix.getMatrix())
r_prdist /= r_prdist.sum()
e_fitprdist /= e_fitprdist.sum()
return r_prdist, xarr, e_fitprdist, (a_final, r_final, sig_final)
# box-bound constraints lb <= x <= ub
lb, ub = -ones(4), ones(4)
# linear inequality constraints
# x0 + x3 <= 0.15
# x1 + x3 <= 1.5
# as Ax <= b
A = mat('1 0 0 1; 0 1 0 1') # tuple, list, numpy array etc are OK as well
b = [0.15, 1.5] # tuple, list, numpy array etc are OK as well
# non-linear constraints
# x0^2 + x2^2 <= 0.15
# 1.5 * x0^2 + x1^2 <= 1.5
c = lambda x: (x[0]**2 + x[2]**2 - 0.15, 1.5 * x[0]**2 + x[1]**2 - 1.5)
p = GLP(f,
lb=lb,
ub=ub,
A=A,
b=b,
c=c,
maxIter=250,
maxFunEvals=1e5,
maxTime=30,
maxCPUTime=30)
r = p.solve('de', mutationRate=0.15, plot=1)
x_opt, f_opt = r.xf, r.ff
fresults.close()
if DB:
try:
DB.results.insert({
"score":best[0],
"date":datetime.datetime.now(),
"params":vars[beta],
"range":rng,
"beta":beta,
"tested_vars":var_names
})
except Exception, e:
print "MONGO INSERT ERROR:%s" % e
return ret
p = GLP(getscore, x0=startPoint, lb=lbs, ub=ubs, maxIter=1000, maxFunEvals=10000)
p.fOpt = 170000 #Optimal value we could have
r = p.maximize('de', iprint=1, plot=0) #, population=10) #, searchDirectionStrategy="best")
#r = p.maximize('galileo', iprint=1, plot=1, population=5)
#r = p.maximize('gsubg', iprint=1, plot=0)
#r = p.maximize('asa', iprint=1, plot=1)
print "Solution vector: %s" % p.xf
print "Max value: %s" % p.ff
theta = [0.2,0.2]
# y = copy.copy(solution[:,1:2])
# y[1::] = y[1::] + numpy.random.normal(loc=0.0,scale=0.1,size=numStep-1)
# odeSIR = odeLossFunc.squareLoss([0.5,1.0/3.0] ,ode,x0,t0,t[1:len(t)],y[1:len(t)],'R')
objSIR = odeLossFunc.squareLoss(theta,ode,x0,t0,t[1::],solution[1::,1:3],['I','R'])
box = [(0.,2.),(0.,2.)]
npBox = numpy.array(box)
lb = npBox[:,0]
ub = npBox[:,1]
pro = GLP(f=objSIR.cost,x0=theta,lb=lb,ub=ub)
pro.plot = True
rGalileo = pro.solve('galileo')
pro = GLP(f=objSIR.cost,x0=theta,lb=lb,ub=ub)
pro.plot = True
rDe = pro.solve('de')
pro = GLP(f=objSIR.cost,x0=theta,lb=lb,ub=ub)
pro.plot = True
rPSwarm = pro.solve('pswarm')
pro = NLP(f=objSIR.cost,df=objSIR.sensitivity,x0=theta,lb=lb,ub=ub)
pro.plot = True
rLincher = pro.solve('lincher')