def graph(self):
self.Posterior_in = MCMC.sampler(self.data_2min_in, samples=15000, mu_init=1.5)
self.Posterior_out = MCMC.sampler(self.data_2min_out, samples=15000, mu_init=1.5)
self.graph_call()
def T0(): data = 2 T = MCMC.MCMC( P0 , data) X, MP , ML = T.M_H(Q0 , 10000 , np.array( [ 10 , 3 ] ) ) mkp0(X)
def initData(self):
# initialize parameter class
try:
param = DataType.paramType()
param.readParams(self.paramFile)
if len(self.paramCovFile) > 0:
param.readCov(self.paramCovFile)
except:
print('WARNING: Error occurred in initializing parameter class.')
raise Exception()
# initialize mcmc class
try:
mcmc_case = MCMC.MCMC_alg()
mcmc_case.init_MCMC(self, param)
except:
print('WARNING: Error occurred in initializing MCMC class.')
raise Exception()
# initialize data class
try:
nObs = len(self.obsDirList)
dataList = np.array([DataType.dataType() for i in range(nObs)])
if len(self.obsVarDirList) > 0: # obsVar file is provided
for i in range(nObs):
dataList[i].readObsData(self.obsDirList[i], self.obsVarDirList[i],
self.simuDirList[i],
self.workPath + '/' + 'config_' + str(i + 1) + '.txt')
else: # no obsVar provided, MIDA will calculate the variance of obs
for i in range(nObs):
dataList[i].readObsData(self.obsDirList[i], '', self.simuDirList[i],
self.workPath + '/' + 'config_' + str(i + 1) + '.txt')
except:
print('WARNING: Error occurred in initializing data class.')
raise Exception()
return [param, mcmc_case, dataList]
def measure():
##Measures and returns our R and M estimate
tr = 2454955.788373
phi = tr * 2 * np.pi / (3.55)
t, rvel = read_rv()
DI = 0.0043
Rstar = 1.79
Rp = np.sqrt(Rstar**2 * DI)
print(Rp)
x0 = [3.55, 4.34505429e+06, 2.50998989e+02]
opt = MCMC.MCMC(lsq, [t, rvel])
opt.M_H(Q, 5000, x0)
print(opt.MAP, opt.MAPL)
plot_fit(t, rvel, opt.MAP)
vp = opt.MAP[2] * u.m / u.s
Mstar = 1.35 * u.M_sun
pstar = Mstar * vp
p_planet = pstar
T = opt.MAP[0] * u.day
m_planet = T**2 * (p_planet**6) / (4 * np.pi**2 * (const.G * Mstar)**2)
m_planet = m_planet**(1.0 / 6)
print(m_planet.to(u.M_sun))
def PART_1():
# Generate clean data.
data_x_1 = np.random.uniform(x_min_1, x_max_1, N_points_1)
data_y_1 = A_1*data_x_1 + B_1
# Add noise.
data_x_1 += lib_distrib.gen_distrib (lib_distrib.Gauss, (0, dx_1), -dx_factor_1*dx_1, dx_factor_1*dx_1, 0, lib_distrib.Gauss(0, (0, dx_1)), N_points_1)
data_y_1 += lib_distrib.gen_distrib (lib_distrib.Gauss, (0, dy_1), -dy_factor_1*dy_1, dy_factor_1*dy_1, 0, lib_distrib.Gauss(0, (0, dy_1)), N_points_1)
# Plot the generated data.
plot_initial_data_1 (data_x_1, data_y_1)
# Perform the MCMC procedure.
data_1 = MCMC.MCMC (linear, (0,0), data_x_1, data_y_1, dp_1, dp_decay_1, N_coarse_1, N_fine_1, N_final_1, N_logging)
# Retrieve the relevant data (the last N_final_1 batches):
data_final_1 = data_1[N_coarse_1+N_fine_1+1:N_coarse_1+N_fine_1+N_final_1+1]
# Calculate and output the optimal A, B values:
A_1_opt, B_1_opt = np.median([d[1][0] for d in data_final_1]), np.median([d[1][1] for d in data_final_1])
print "Optimal linear parameter values: A = ", A_1_opt, ", B = ", B_1_opt
# Calculate the acceptance rates for all 3 modes. Print them out.
acc_rates = calc_acceptance_rates ([d[2] for d in data_1[1:N_coarse_1+1]], [d[2] for d in data_1[N_coarse_1+1:N_coarse_1+N_fine_1+1]], [d[2] for d in data_final_1])
print "Acceptance rate for the Coarse mode: ", round(acc_rates[0]*100, 2), "%."
print "Acceptance rate for the Fine mode: ", round(acc_rates[1]*100, 2), "%."
print "Acceptance rate for the Final mode: ", round(acc_rates[2]*100, 2), "%."
# Plot the posterior distribution for A, B and both. Only for the Final mode.
plot_distr ([[d[1][0] for d in data_final_1], [d[1][1] for d in data_final_1]], ['A','B'], 1)
# Plot the cumulative sum graph and calculate 68% and 95% confidence intervals.
plot_cumul ([[d[1][0] for d in data_final_1],[d[1][1] for d in data_final_1]], ['A','B'], 1, [0.68, 0.95])
def T1(): data = np.random.poisson(3 , 1000) T = MCMC.MCMC(P1 , data) X , MP , ML = T.M_H(Q1 , 10000 , np.array( [ 5 ] ) ) mkp1(X) print (MP , ML)
def generateMCMC(filename):
a = mcmc.MCMC()
a.setSteps(100000)
a.setSigmas(sigma)
a.current_point = mean
a.setLogLikelihoodFunction(logp)
a.loop()
f = open(filename, 'wb')
pickle.dump(a, f)
f.close()
return a
def main():
while True:
print("""
指令列表如下：
1.查看不同题目作答组合的L曲线
2.对题目作答进行DSY算法估计
3.对题目作答进行MCMC算法估计
4.导入xls类型的作答结果并对其进行分析和处理
0.退出
""")
command = input('请输入需要执行的指令')
a, b = Init_MIRT.Init_a_b()
if command == '0':
print('感谢您的使用')
break
elif command == '1':
time_star=time.time()
Show_L.m_show(a, b)
time_end=time.time()
print("程序运行时间：%.8s s" %(time_end-time_star))
elif command == '2':
time_star = time.time()
MIRT_DSY.DSY(a, b)
time_end = time.time()
print("程序运行时间：%.8s s" % (time_end-time_star))
elif command == '3':
time_star = time.time()
MCMC.MCMC(a,b)
time_end = time.time()
print("程序运行时间：%.8s s" % (time_end-time_star))
elif command == '4':
print("""
请输入需要处理的文件位置
""")
while True:
URL=input()
if URL=='':
print("请输入有效地址")
else:
print('测试完成，本功能还在开发中')
break
print('finish')
KEY=input('继续执行请按1，停止执行请按0')
if (KEY!='1'):
break
def get_birdcounts_sample(datafile,
loglikelihood,
poly_deg,
dof=4,
pc=4,
maxruns=50000):
bc = pd.read_csv(datafile, index_col=0)
#bc = bc.drop("Total",axis=1)
N = len(bc)
lbd = 10. / numpy.sqrt((poly_deg + 1) * (N))
sigma = numpy.eye((poly_deg + 1) * N)
time = numpy.array([int(x) for x in bc.columns], dtype=float)
time = Seasonal_ODE.time_transform(time)
bc_mat = bc.as_matrix()
dof = 4
pc = 4
init_guess = bc_init_guess(datafile, poly_deg)
p_vals = numpy.zeros((N, len(time)))
amean = numpy.zeros(N)
bmean = numpy.zeros(N)
coeff_mean = numpy.zeros((N, poly_deg + 1))
coeff = []
for i in range(N):
loglikargs = (bc_mat[i], time)
theta_bc, k_bc = MCMC.run_MCMC_convergence(init_guess[i, :],
loglikelihood,
loglikargs,
maxruns=maxruns,
pc=4,
method="Nelder-Mead")
n = len(bc_mat[i])
results = theta_bc[0][::10]
#coeff = numpy.zeros((len(results),poly_deg+1))
coeff.append(numpy.zeros((len(results), poly_deg + 1)))
for j in range(poly_deg + 1):
#coeff[:,j,numpy.newaxis] = results[:,j::poly_deg+1]
coeff[-1][:, j, numpy.newaxis] = results[:, j::poly_deg + 1]
#coeff_mean[i,:] = numpy.mean(coeff,axis=0)
coeff_mean[i, :] = numpy.mean(coeff[-1], axis=0)
return (coeff_mean, coeff)
def PART_2():
# Retrieve the data set.
data_x_2 = Data_part_2.x
data_y_2 = Data_part_2.y
# Plot the retrieved data.
plot_initial_data_2 (data_x_2, data_y_2)
# Perform the MCMC procedure.
data_2 = MCMC.MCMC (sinusoidal, (0,0,0), data_x_2, data_y_2, dp_2, dp_decay_2, N_coarse_2, N_fine_2, N_final_2, N_logging)
# Retrieve the relevant data (the last N_final_1 batches):
data_final_2 = data_2[N_coarse_2+N_fine_2+1:N_coarse_2+N_fine_2+N_final_2+1]
# Calculate and output the optimal A, B, C values:
A_2_opt, B_2_opt, C_2_opt = np.median([d[1][0] for d in data_final_2]), np.median([d[1][1] for d in data_final_2]), np.median([d[1][2] for d in data_final_2])
print "Optimal sinusoidal-linear parameter values: A = ", A_2_opt, ", B = ", B_2_opt, ", C = ", C_2_opt
# Calculate the acceptance rates for all 3 modes. Print them out.
acc_rates = calc_acceptance_rates ([d[2] for d in data_2[1:N_coarse_2+1]], [d[2] for d in data_2[N_coarse_2+1:N_coarse_2+N_fine_2+1]], [d[2] for d in data_final_2])
print "Acceptance rate for the Coarse mode: ", round(acc_rates[0]*100, 2), "%."
print "Acceptance rate for the Fine mode: ", round(acc_rates[1]*100, 2), "%."
print "Acceptance rate for the Final mode: ", round(acc_rates[2]*100, 2), "%."
# Plot the posterior distribution for A, B and both. Only for the Final mode.
plot_distr ([[d[1][0] for d in data_final_2], [d[1][1] for d in data_final_2], [d[1][2] for d in data_final_2]], ['A','B','C'], 2)
# Plot the cumulative sum graph and calculate 68% and 95% confidence intervals.
plot_cumul ([[d[1][0] for d in data_final_2], [d[1][1] for d in data_final_2], [d[1][2] for d in data_final_2]], ['A','B','C'], 2, [0.68, 0.95])
# Plot the predicted function over the initial dataset.
plot_part_2_result (data_x_2, data_y_2, sinusoidal, (A_2_opt, B_2_opt, C_2_opt))
def get_bloodmeal_sample(datafile,
loglikelihood,
poly_deg,
dof=4,
pc=4,
maxruns=50000):
bm = pd.read_csv(datafile, index_col=0)
#bm=bm.drop("Total",axis=1)
N = len(bm)
time = numpy.array([int(x) for x in bm.columns], dtype=float)
time = Seasonal_ODE.time_transform(time)
init_guess = numpy.zeros((poly_deg + 1) * (N - 1))
loglikargs = (bm.as_matrix(), time)
#the_0 = MCMC.sample_dist(init_guess,pc,loglikelihood,loglikargs)
theta_bm, k_bm = MCMC.run_MCMC_convergence(init_guess,
loglikelihood,
loglikargs=(bm.as_matrix(),
time),
maxruns=maxruns,
pc=4)
n = len(bm.as_matrix())
results = theta_bm[0][::10]
coeff_mean = numpy.zeros((N - 1, poly_deg + 1))
for j in range(poly_deg + 1):
coeff_mean[:, j] = numpy.mean(results[:, j::poly_deg + 1], axis=0)
# a = results[:,0::2]
# b = results[:,1::2]
# a0= numpy.percentile(a,5,axis=0)
# a1= numpy.percentile(a,95,axis=0)
# amean = numpy.mean(a,axis=0)
# b0= numpy.percentile(b,5,axis=0)
# b1= numpy.percentile(b,95,axis=0)
# bmean = numpy.mean(b,axis=0)
return (coeff_mean, results)
T = 3 # The length of MCMC is T
t = 0
Para = Function.GeneratePara(t, Para0=None, D=None, P=None) # Initialize Para
D = None
P = None # Get D1 and P1
df = 1
# Begin to find the best Para and its relevant parameters D, chi2 Cov etc-----------------------------------------------
t += 1
ParaSet = array(Para) # The set of the accepted Para
chi2 = Function.chi2(Para, Data, EoS)
chi2Set = array([chi2
]) # The set of the chi2 corresponding to the accepted Para
Accept = array([1]) # The set of the Accept corresponding to the accepted Para
while t <= T:
[Para, chi2, D, P, ParaSet, chi2Set, Accept, mu, Cov] = \
MCMC.MarkovChain(Data, EoS, Para, chi2, D, P, ParaSet, chi2Set, Accept, t)
t += 1
CI = Function.CI(df, chi2)
[index, ProbabilityDensity, Probability] = Function.CIindex(CI, Accept)
Deviation = abs(Para - ParaSet[index])
# The NS's maximum mass and its upper limits and lower limits ----------------------------------------------------------
TOV_output = Function.TOV(Para, EoS)
M_NS_max = max(TOV_output[2])
[Para_Uplims, Para_Lolims, M_NS_max_Uplims,
M_NS_max_Lolims] = Para_Uplims_Lolims(Para, Deviation, EoS, M_NS_max)
End = time.clock()
TimeUsed = End - Start
# Output Result --------------------------------------------------------------------------------------------------------
ResultDir = os.getcwd() + '/Result/'
return odeint(LotkaVolterra,state0,t, args=(alpha,beta,gamma, delta))
def chi_2 (tiempos, X_obs, params):
x_obs =X_obs[0]
y_obs =X_obs[1]
chi2_1 = sum((x_obs - my_model(tiempos,params)[:,0])**2)
chi2_2 = sum((y_obs - my_model(tiempos,params)[:,1])**2)
return chi2_1+chi2_2
guess = [30,5,50,2]
step_size = [0.01,0.01,0.01,0.01]
n_params = 4
n_points = 1000
best, walk, chi2 = MCMC.hammer(tiempos,[x_obs , y_obs] , guess, chi_2, step_size ,n_params, n_points)
print "El valor de alpha es", best[0]
print "El valor de beta es", best[1]
print "El valor de gamma es", best[2]
print "El valor de delta es", best[3]
f1=open('valores.dat', 'w+')
for i in range(n_points):
f1.write('%f %f %f %f %f\n' %(walk[0,i], walk[1,i], walk[2,i], walk[3,i],chi2[i]))
#UNCERTAINTIES: SELECCIONO UNOS CUANTOS VALORES QUE SATISFAGAN LAS CONDICIONES PEDIDAS:
# alpha_doublepl = alpha*(c**(tau-sigma))/tau
# t = (sigma*size/alpha_doublepl)**(1/sigma) # size è quella finale o originale?
# u = TruncPois.tpoissrnd(t*w0)
t = (sigma * size / alpha)**(1 / sigma)
u = TruncPois.tpoissrnd(t * w)
n = Updates.update_n(w, G, p_ij) # sui vecchi o nuovi w?
# output = MCMC("w_gibbs", "exptiltBFRY", iter, sigma=sigma_true, tau=tau_true, alpha=alpha_true, u=u_true,
# p_ij=p_ij, n=n_true)
output = MCMC("w_gibbs",
"GGP",
iter,
sigma_tau=0.08,
tau=tau,
sigma=sigma,
alpha=alpha,
u=u,
n=n,
p_ij=p_ij,
c=c,
w_init=w)
# output = MCMC("w_HMC", "exptiltBFRY", iter, epsilon=epsilon, R=R,
# tau=tau_true, sigma=sigma_true, alpha=alpha_true, u=u_true, n=n_true, p_ij=p_ij, w_init=w)
output = MCMC("w_HMC",
"GGP",
iter,
epsilon=epsilon,
R=R,
tau=tau,
sigma=sigma,
alpha=alpha,
def chi_2(tiempos, X_obs, params):
x_obs = X_obs[0]
y_obs = X_obs[1]
chi2_1 = sum((x_obs - my_model(tiempos, params)[:, 0])**2)
chi2_2 = sum((y_obs - my_model(tiempos, params)[:, 1])**2)
return chi2_1 + chi2_2
guess = [30, 5, 50, 2]
step_size = [0.01, 0.01, 0.01, 0.01]
n_params = 4
n_points = 1000
best, walk, chi2 = MCMC.hammer(tiempos, [x_obs, y_obs], guess, chi_2,
step_size, n_params, n_points)
print "El valor de alpha es", best[0]
print "El valor de beta es", best[1]
print "El valor de gamma es", best[2]
print "El valor de delta es", best[3]
f1 = open('valores.dat', 'w+')
for i in range(n_points):
f1.write('%f %f %f %f %f\n' %
(walk[0, i], walk[1, i], walk[2, i], walk[3, i], chi2[i]))
#UNCERTAINTIES: SELECCIONO UNOS CUANTOS VALORES QUE SATISFAGAN LAS CONDICIONES PEDIDAS:
plt.scatter(tiempos, y_obs, c='g')
###### Calculate the total number of datapoints
datapoints = 0
for phase in spectra_observed.keys():
for spectrum in spectra_observed[phase].keys():
datapoints += len(spectra_observed[phase][spectrum])
parameters['OTHER']['total_datapoints'] = datapoints
"""
==================
Main MCMC sampling
==================
"""
###### Set the initial positions of the walkers ################################
parameters, parameters_init = \
MCMC.mcmc_initial_positions(parameters,
prev_chain=parameters['OTHER']['previous_chain'],
dir_previous_chain=parameters['OTHER']['dir_previous_chain'])
###### Check if the priors are in the accepted range ###########################
for walker in range(parameters['OTHER']['n_walkers']):
parameters_add = MCMC.calc_additional_par(parameters,
parameters_init[walker, :])
while MCMC.ln_prior(parameters_init[walker, :], parameters,
parameters_add) == -np.inf:
pars, parameters_init[walker, :] = MCMC.mcmc_initial_positions(
parameters, single_walker=True)
parameters_add = MCMC.calc_additional_par(parameters,
parameters_init[walker, :])
def main(argv):
t0 = time.time()
filename = 'test.pkl'
nStep = 10000
nThreads = 1
dirname = './'
matrix = ''
alpha = 0
try:
opts, args = getopt.getopt(argv, "f:n:t:a:d:m:")
except getopt.GetoptError:
print 'test.py -i <inputfile> -o <outputfile>'
sys.exit(2)
for opt, arg in opts:
if opt == '-f':
filename = arg
elif opt == '-n':
nStep = int(arg)
elif opt == '-t':
nThreads = int(arg)
elif opt == '-a':
alpha = float(arg)
elif opt == '-d':
dirname = arg
model = load_model("datasets/R_resolution.csv",
"datasets/B_resolution.csv")
#observed = np.loadtxt("datasets/observed_mock_equal.txt")
fluxD = 100 + np.array([2 * i for i in range(model.nBinsBT)])
fluxP = 100 + np.array([2 * i for i in range(model.nBinsBT)])
# fluxP = 100 + np.zeros(model.nBinsBT)
flux = np.concatenate([fluxP, fluxD])
observed = make_mock_observation(fluxP, fluxD)
def logp(value):
value = np.array(value)
if (value < 0).any(): return -np.inf
# value must be and array twice the size of binning
expected = model(*value.reshape((2, model.nBinsBT)))
log = (observed * np.log(expected) - expected).sum()
# Didn't figure that out yet
#firstDerivative = np.diff(np.log(value))
#secondDerivative = np.fabs(np.diff(firstDerivative))
#smoothness = -(alpha * secondDerivative).sum()
return log #+ smoothness
sigma = 5
def proposal_function(previous_point):
point = np.zeros(len(previous_point))
#return previous_point+self.sigma*np.random.standard_normal(self.nVar)
for i in range(len(previous_point)):
while True:
val = previous_point[i] + 0.01 * np.random.standard_normal()
if val > 0:
point[i] = val
break
return point
filename = 'alpha{}_'.format(alpha) + filename
threads = []
for i in range(nThreads):
theFileName = dirname + '/thread{}_'.format(i) + filename
a = MCMC.MCMC(theFileName,
initialCondition=flux[:],
realValues=flux[:])
a.setProposalFunction(proposal_function)
a.setLogLikelihoodFunction(logp)
a.setSteps(nStep)
threads.append(a)
for t in threads:
print 'launching thread'
t.start()
time.sleep(1)
for t in threads:
t.join()
print 'done'
print 'time : {}'.format(time.time() - t0)
def runShatellite(numOfSlices,
Acloud,
rateDiss,
speedCloud,
w,
ndata,
fastFoward,
Days,
nwalkers,
nsamples,
nsteps,
timespan,
phispan,
burning,
plot=True,
mcmc=True):
#Maximum number of slices is hPerDayHours
hPerDay = int((w / (2 * np.pi))**(-1))
if (numOfSlices > hPerDay):
print("Cannot have more than 24 number of slices for now")
return 0, 0
#Generate the initial condition of the planet
surf = M_init.initialPlanet(numOfSlices, False)
clouds = M_init.cloudCoverage(numOfSlices)
finalTime = []
apparentTime = []
l, d = dataAlbedoDynamic(numOfSlices,
Days,
w,
Acloud,
surf,
clouds,
rateDiss,
speedCloud,
Animation=False)
print("Got sum fake data. YOHO, SCIENCE BITCH!")
for i in range(1, Days + 1):
#Seperates the effective albedo and longitude per day.
effective = d[(i - 1) * numOfSlices:(i) * (numOfSlices)]
lon = l[(i - 1) * numOfSlices:(i) * (numOfSlices)]
#Calculates the apparent albedo with the forward model.
time, apparent = M_Init.apparentAlbedo(effective,
time_days=timespan,
long_frac=phispan,
n=5000,
plot=False,
alb=True)
finalTime.append(time + (hPerDay * (i - 1)))
apparentTime.append(apparent)
finalTime = np.asarray(finalTime).flatten()
apparentTime = np.asarray(apparentTime).flatten()
t, a = extractN(finalTime, apparentTime, ndata * Days)
print("Done extracting {}".format(numOfSlices))
#Plotting
if plot:
fig, ax = plt.subplots(1,
1,
gridspec_kw={'height_ratios': [1]},
figsize=(10, 8))
for i in range(Days + 1):
ax.axvline((i) * hPerDay, color='orange', alpha=1, zorder=10)
ax.plot(finalTime,
apparentTime,
'-',
color='black',
linewidth=5,
label="Simulated curve")
ax.errorbar(t,
a,
fmt='.',
color='green',
yerr=np.asarray(a) * 0.02,
markersize=8,
solid_capstyle='projecting',
capsize=4,
label="selected {} data".format(ndata))
ax.set_xlabel("Time (h)", fontsize=22)
ax.set_ylabel("Apparent Albedo ($A^*$)", fontsize=22)
ax.tick_params(labelsize=22)
ax.legend(fontsize=15)
chainArray = []
alb = []
if (mcmc):
#Implement the MCMC running stuff in a seperate function
for i in range(1, Days + 1):
time = t[(i - 1) * ndata:i * ndata]
app = a[(i - 1) * ndata:i * ndata]
#Maybe this is wrong, check this, fix this stuff
lon = np.asarray(l[(i - 1) * numOfSlices:(i) * (numOfSlices)])
lon = [l % (360) for l in lon]
lon[lon == 0] = 360
m.MCMC(nwalkers, nsteps, numOfSlices, time, app, lon, timespan,
phispan, burning, hPerDay, chainArray, i, ax, plot)
print("done MCMC for day {}".format(i))
for chain in chainArray:
alb.append(m.mcmc_results(chain, burning))
return alb
def runSatellowan(numOfSlices,
Acloud,
npara,
rateDiss,
speedCloud,
w,
ndata,
fastFoward,
Days,
nwalkers,
nsamples,
nsteps,
timespan,
phispan,
burning,
plot=True,
mcmc=True,
repeat=False,
walkers=False,
forming=True,
Epic=None):
#Need to make this a bit more efficient)
ndim = numOfSlices
hPerDay = int((w / (2 * np.pi))**(-1))
if plot:
fig, ax = plt.subplots(1,
1,
gridspec_kw={'height_ratios': [1]},
figsize=(10, 4))
if type(Epic) == type(None):
#if (numOfSlices>24):
# print ("Cannot have more than 24 number of slices for now")
# return 0,0
surfDict = M_init.initialPlanet(numOfSlices, plot=True)
surf = np.fromiter(surfDict.values(), dtype=float)
surf = [0.458, 0.327, 0.332, 0.263]
print("The planet's surface albedo is theoritically", surf)
clouds = M_init.cloudCoverage(numOfSlices)
clouds = [0, 0, 0, 0]
print(
"The effective albedo is ",
M_init.effectiveAlbedo(numOfSlices,
Acloud,
plot=False,
calClouds=clouds,
calsurf=surf))
finalTime = []
apparentTime = []
print(clouds, "Cloud coverage is ")
d = dataAlbedoDynamic(numOfSlices,
Days,
w,
Acloud,
surf,
clouds,
rateDiss,
speedCloud,
Animation=False,
hourlyChange=False,
repeat=repeat,
forming=forming)
for i in range(1, Days + 1):
effective = d[(i - 1) * numOfSlices:(i) * (numOfSlices)]
print("The albedo map for day {} is ".format(i - 1), effective)
#start = tyme.time()
time, apparent = M_init.apparentAlbedo(effective,
time_days=timespan,
long_frac=phispan,
phi_obs_0=0,
n=10000,
plot=False,
alb=True)
#tim_comp, app_comp = ck_lib.lightcurve(effective,time_days=timespan,
# long_frac=phispan,phi_obs_0=0,n=10000,plot=False,alb=True)
#end = tyme.time()
#print (end-start)
finalTime.append(time + (hPerDay * (i - 1)))
apparentTime.append(apparent)
finalTime = np.asarray(finalTime).flatten()
apparentTime = np.asarray(apparentTime).flatten()
t, a = extractN(finalTime, apparentTime, ndata, Days)
noise = [
np.random.normal(loc=0, scale=0.02 * a[i]) for i in range(len(a))
]
a = np.array(a) + np.array(noise)
if plot:
fig, ax = plt.subplots(1,
1,
gridspec_kw={'height_ratios': [1]},
figsize=(10, 3))
tim, albedo = drawAlbedo(d, Days, 5000)
ax.errorbar(t,
a,
fmt='.',
yerr=0.02 * np.array(a),
color='black',
markersize=8,
label="Simulated lightcurve",
solid_capstyle='projecting',
capsize=4)
#ax.plot(tim_comp,app_comp,'.',color='orange',linewidth=4,label="Early Version of F.M.")
#ax.plot(tim,albedo,color='purple',linewidth=6,alpha=0.6,label=r'$A_{T.O.P}(\phi)$')
#ax.plot(t,a,'.',color='purple',label='Albedo Generated for {} slices'.format(numOfSlices),alpha=0.3)
ax.set_xlabel("Time (h)", fontsize=22)
ax.set_ylabel("Apparent Albedo ($A^*$)", fontsize=22)
#ax.legend(fontsize=17)
ax.tick_params(labelsize=22)
else:
t = Epic[0]
a = Epic[1]
t = (t - t[0]) * 24
ax.errorbar(t,
a,
fmt='.',
yerr=Epic[3],
color='black',
markersize=8,
label="EPIC data",
solid_capstyle='projecting',
capsize=4)
print("Done extracting {}".format(numOfSlices))
chainArray = []
alb = []
if plot:
#ax.errorbar(t,a,fmt='.',color='blue',yerr = np.asarray(a)*0.02,markersize=10,solid_capstyle='projecting', capsize=4,
# label= "Raw Data from EPIC")
ax.set_xlabel("Time (h)", fontsize=22)
ax.set_ylabel("Apparent Albedo ($A^*$)", fontsize=22)
if type(Epic) != type(None):
title = r"EPIC data [$d$ = {}] ".format(util.date_after(Epic[2]))
#title = r"Forward model for {} slice albedo map".format(numOfSlices)
ax.set_title(title, fontsize=22)
ax.legend(fontsize=20)
ax.tick_params(labelsize=25)
if (mcmc):
#Implement the MCMC running stuff in a seperate function
for i in range(1, Days + 1):
time = t[(i - 1) * ndata:i * ndata]
app = a[(i - 1) * ndata:i * ndata]
chain = m.make_chain(nwalkers,
nsteps,
ndim,
time,
app,
timespan,
phispan,
alb=True)
chainArray.append(chain)
print(
"Well call me a slave, because I just made some chains for day {}..."
.format(i))
mean_mcmc_params = m.mcmc_results(chain, burning)
mean_mcmc_time, mean_mcmc_ref = M_init.apparentAlbedo(
mean_mcmc_params,
time_days=timespan,
long_frac=phispan,
n=10000,
plot=False,
alb=True)
print("Got the mean MCMC results for day {}. Ya YEET!".format(i))
flat = m.flatten_chain(chain, burning)
sample_params = flat[np.random.randint(len(flat), size=nsamples)]
for s in sample_params:
sample_time, sample_ref = M_init.apparentAlbedo(
s,
time_days=timespan,
long_frac=phispan,
n=10000,
plot=False,
alb=True)
sample_time = np.asarray(sample_time)
mean_mcmc_params = np.asarray(mean_mcmc_params)
plotting_x = np.asarray(sample_time) + (i - 1) * hPerDay
if (plot):
ax.plot(plotting_x, sample_ref, color='k', alpha=0.1)
if (plot):
ax.plot(plotting_x,
sample_ref,
color='k',
alpha=0.1,
label='50 samples from MCMC')
ax.plot(mean_mcmc_time + (i - 1) * hPerDay,
mean_mcmc_ref,
color='red',
label="Mean MCMC")
ax.legend(fontsize=20)
#aic = Aic(app,mean_mcmc_ref,npara)
#bic = Bic(app,mean_mcmc_ref,npara,ndata)
print("done MCMC for day {}".format(i))
if plot:
plt.show()
counter = 0
effmean = []
#hour = dt.datetime.now().time()
#fileName = hour.strftime("%H:%M:%S").replace(":","_",2)
#f= open("MCMC_{}__{}.csv".format(fileName,numOfSlices),"w+")
#f.write(''.join(str(effectiveAlbedo(numOfSlices,Acloud,plot=False,calClouds=clouds,calsurf=surf)).replace("[","",1).replace("]","",1))+"\n")
for chainy in chainArray:
results = m.mcmc_results(chainy, burning)
if (walkers):
m.plot_walkers_all(chainy, expAlb=None)
m.cornerplot(chainy, burning)
plt.show()
alb.append(results)
print("The result for day {} is".format(counter), results)
#f.write(''.join(str(results).replace("[","",1).replace("]","",1))+"\n")
effmean.append(np.mean(results))
counter += 1
#f.close()
if (plot):
x = np.arange(counter)
mean = np.mean(effmean)
error = np.std(effmean) / np.sqrt(len(effmean))
fig, ax = plt.subplots(1,
1,
gridspec_kw={'height_ratios': [1]},
figsize=(10, 8))
ax.plot(x, effmean, '.', markersize=8, color='purple')
ax.axhline(np.mean(
M_init.effectiveAlbedo(numOfSlices,
Acloud,
plot=False,
calClouds=clouds,
calsurf=surf)),
linewidth=8,
color='orange',
label='Expected Mean')
ax.axhline(mean + error, linewidth=8, color='purple', alpha=0.3)
ax.axhline(mean - error, linewidth=8, color='purple', alpha=0.3)
ax.axhline(mean, linewidth=8, color='purple', label='Found Mean')
ax.set_xlabel("Day", fontsize=22)
ax.set_ylabel("Average albedo from MCMC", fontsize=22)
ax.legend(fontsize=15)
plt.show()
minAlb = minimumAlb(alb)
return alb, minAlb, surf
def chi_2 (x_obs, y_obs, params):
chi2 = sum((y_obs - my_model(x_obs,params))**2)
return chi2
datos = np.loadtxt("energy_counts.dat")
x_obs = datos[:,0]
y_obs = datos[:,1]
guess = [5*(10**16), 1000, 1400, 10**2, -2]
step_size = [5*10**14, 10, 0.1, 0.1, 0.01]
n_params = 5
n_points = 1000000
best, walk, chi2 = MCMC.hammer(x_obs, y_obs, guess, chi_2, step_size ,n_params, n_points)
print "El valor de A es", best[0]
print "El valor de B es", best[1]
print "El valor de E0 es", best[2]
print "El valor de sigma es", best[3]
print "El valor de alpha es", best[4]
plt.plot(walk[1,:],chi2)
plt.xlabel('$\\alpha$')
plt.ylabel('$\chi^2$')
plt.title('$\chi^2$ vs. $\\alpha$')
plt.savefig("x2vsalpha.pdf")
plt.close()
plt.plot(walk[0,:],walk[1,:])
plt.xlabel('$A$')
def chi_2(x_obs, y_obs, params):
chi2 = sum((y_obs - my_model(x_obs, params))**2)
return chi2
datos = np.loadtxt("energy_counts.dat")
x_obs = datos[:, 0]
y_obs = datos[:, 1]
guess = [5 * (10**16), 1000, 1400, 10**2, -2]
step_size = [5 * 10**14, 10, 0.1, 0.1, 0.01]
n_params = 5
n_points = 1000000
best, walk, chi2 = MCMC.hammer(x_obs, y_obs, guess, chi_2, step_size, n_params,
n_points)
print "El valor de A es", best[0]
print "El valor de B es", best[1]
print "El valor de E0 es", best[2]
print "El valor de sigma es", best[3]
print "El valor de alpha es", best[4]
plt.plot(walk[1, :], chi2)
plt.xlabel('$\\alpha$')
plt.ylabel('$\chi^2$')
plt.title('$\chi^2$ vs. $\\alpha$')
plt.savefig("x2vsalpha.pdf")
plt.close()
plt.plot(walk[0, :], walk[1, :])
plt.xlabel('$A$')
import MCMC
import numpy as np
print("Hello!")
J = 3
s = MCMC.State(np.array(range(J)) * 1.0, np.array(range(J)), np.zeros(3), 0.0)
print(s)
print(type(s))
print(s.alpha)
for a in s.alpha:
print(a)
def fieldnames(x):
return list(filter(lambda xi: xi[0:2] != '__', x.__dir__()))
fieldnames(s)
MCMC.cmodel(np.random.randn(100), 10, s, {'N': 100}, nmcmc=1000, nburn=1000)
''' Concatyente Poisson means '''
out = np.empty(len(disasters_array))
out[:s] = e
out[s:] = l
return out
9/8:
@deterministic(plot=False)
def rate(s=switchPoint, e=early_mean, l=late_mean):
''' Concatyente Poisson means '''
out = np.empty(len(disasters_array))
out[:s] = e
out[s:] = l
return out
9/9: disasters = Poisson('disasters', mu=rate, value=disasters_array, observed=True)
9/10: from pymc import MCMC
9/11: M = MCMC(disasters)
9/12: M.sample(iter=10000, burn=1000, thin=10)
9/13: M.trace('switchPoint')[:]
9/14: M.trace('switchpoint')[:]
10/1: fromm open
10/2: from opencv2
12/1: import cv2 as cv
13/1: import scipy.io
13/2: from scipy import io
13/3: import scipy
14/1:
class neuraNetwork:
def __init__():
pass
def train():
tstart = Seasonal_ODE.time_transform(90) # Setting Start Time to April 1st
tend = Seasonal_ODE.time_transform(270)
flag = 2
write_flag = 0 # If set to 0 will write the results, if set to 1 will not
if flag == 0: # This section runs the MCMC for the various areas of interest, and stores the results
mos_coeff, mos_results = bloodmeal.vector_coeff(
msq_file, MCMC.poly_poiss_log_lik, poly_deg, maxruns=maxruns)
bm_coeff_mat, bm_results = bloodmeal.get_bloodmeal_sample(
bm_file,
MCMC.bm_polynomial_loglikelihood,
poly_deg,
maxruns=maxruns)
bc_coeff_mat, bc_results = BirdCount.get_birdcounts_sample(
bc_file, MCMC.poly_poiss_log_lik, poly_deg, maxruns=maxruns)
#BirdCount.BirdcountTest(bc_file,bc_coeff_mat,poly_deg)
bc_DIC = MCMC.get_DIC(bc_results, MCMC.poly_poiss_log_lik, bc_file)
bm_DIC = MCMC.DIC(bm_results, MCMC.bm_polynomial_loglikelihood,
bm_data, Seasonal_ODE.time_transform(bm_time))
mos_DIC = MCMC.get_DIC(mos_results, MCMC.poly_poiss_log_lik, msq_file)
if write_flag == 0:
with open('Mos_coeff_poly_deg(%d).pkl' % poly_deg, 'wb') as output:
pickle.dump(mos_coeff, output)
with open('bloodmeal_coeff_poly_deg(%d).pkl' % poly_deg,
'wb') as output:
pickle.dump(bm_coeff_mat, output)
with open('host_coeff_poly_deg(%d).pkl' % poly_deg,
'wb') as output:
pickle.dump(bc_coeff_mat, output)
continue
time.append(float(i.split()[0]))
flux.append(float(i.split()[1]))
return time, flux
t, f = read_lightcurve("lightcurve_data.txt")
x0 = [3.5, 2.2, .1, 0.3] ##A reasonable initial guess
r = [3.546, 2.25, .007,
.15] ##This is my current estimate for our best solution
opt = MCMC.MCMC(P, [t, f])
X, M, ML = opt.M_H(
Q2, 5000, r
) ##Lots of iterations, so somewhat slow. Good chance to find the right answer.
print(opt.MAP, opt.MAPL)
plot_fit(opt.MAP, [t, f])
p_list = []
di_list = []
for i in X[500::]:
p_list.append(i[0])
di_list.append(i[2])
import plotting as p
import experiments as e
import MCMC as m
import matplotlib.pyplot as plt
# pass the path where Submission folder is saved.
path = "C:/Users/Shruti Jadon/Desktop/590_HW3/"
J = np.array([0, 1, 1, 0, 0, 0, 1, 0])
B = np.array([1, 1, 0, 1, 1, 0, 0, 0])
#(F.) output
J = np.array([0, 0, 1, 1, 1]) # pass the J, B and alpha Values
B = np.array([1, 1, 0, 0, 1])
alpha = 0.6
output = m.MetropolisJsampling(
J, B, alpha
) # call metropolis J sampling function of normal distribution, and normal J sampling by chosing one random bit flipping
print "output of (f.) question. i.e. Jar Values"
print output # print values in console
p.BarGraph(output, path, "output of (f.) question") # plot graph of
#(F.) running Experiment of J_random to check if we get same output or not.
output_experiment = e.MC_Jar_Experiment(
J, B, alpha) # calling experiment metropolis Sampling question
print "output_experiment values"
print output_experiment
p.BarGraph(
output_experiment, path,
"Experimental output of (f.) question") # plotting graph of Experiment
#(H.) output