def fit(Deltam,
nsne,
xi,
redshiftterm,
mpi=False,
p0=None,
nchain=2000,
**kwargs):
ndim, nwalkers = 4, 8
sig = numpy.array([0.1, 0.01, 0.01, 50 / 3e5])
if p0 is None:
p0 = [
numpy.array([1, 0, 0.08, 200 / 3e5]) +
numpy.random.uniform(low=-sig, high=sig)
for i in range(nwalkers)
]
if mpi:
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
else:
import time
starttime = time.time()
print("Start {}".format(starttime))
sampler = emcee.EnsembleSampler(
nwalkers,
ndim,
Fit.lnprob,
args=[Deltam, nsne, xi, redshiftterm],
pool=pool)
else:
import time
starttime = time.time()
print("Start {}".format(starttime))
sampler = emcee.EnsembleSampler(
nwalkers,
ndim,
Fit.lnprob,
args=[Deltam, nsne, xi, redshiftterm])
sampler.run_mcmc(p0, nchain)
if mpi:
if pool.is_master():
endtime = time.time()
print("End {}".format(endtime))
print("Difference {}".format(endtime - starttime))
pool.close()
else:
endtime = time.time()
print("End {}".format(endtime))
print("Difference {}".format(endtime - starttime))
return sampler
def mcmc(mass_bins, dot_val, initial_c, nwalkers, ndim, burn_in, steps_wlk):
import numpy as np
import scipy.optimize as op
import emcee
from emcee.utils import MPIPool
import sys
def lnlike(c, dot_val):
loglike = np.zeros((1))
loglike[0] = sum(
np.log(
(1 - c) * np.sqrt(1 + (c / 2)) *
(1 - c * (1 - 3 *
(dot_val * dot_val / 2)))**(-1.5))) #log-likelihood
return loglike
def lnprior(c):
if (-1.5 < c < 0.99): #Assumes a flat prior, uninformative prior
return 0.0
return -np.inf
def lnprob(c, dot_val):
lp = lnprior(c)
if not np.isfinite(lp):
return -np.inf
return lp + lnlike(c, dot_val)
#Parallel MCMC - initiallizes pool object; if process isn't running as master, wait for instr. and exit
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
pos = [initial_c + 1e-2 * np.random.randn(ndim) for i in range(nwalkers)
] #initial positions for walkers "Gaussian ball"
#MCMC Running
sampler = emcee.EnsembleSampler(nwalkers,
ndim,
lnprob,
args=[dot_val],
pool=pool)
pos, _, _ = sampler.run_mcmc(pos,
burn_in) #running of emcee burn-in period
sampler.reset()
sampler.run_mcmc(
pos, steps_wlk
) #running of emcee for steps specified, using pos as initial walker positions
pool.close()
chain = sampler.flatchain[:, 0]
return chain
def run_pool(pC, pW, walk, step): #pCenter and pWidths
steps = step
nwalkers = walk
ndim = len(pC)
## r in, del r, i, PA
p0 = [pC[0], pC[1], pC[2], pC[3]]
widths = [pW[0], pW[1], pW[2], pW[3]]
p = emcee.utils.sample_ball(p0, widths, size=nwalkers)
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
sampler = emcee.EnsembleSampler(nwalkers,
ndim,
lnlike_vis_and_sed,
live_dangerously=True,
pool=pool)
print 'Beginning the MCMC run.'
start = time.clock()
sampler.run_mcmc(p, steps)
stop = time.clock()
pool.close()
print 'MCMC finished successfully.\n'
print 'This was a simultaneous visibility and SED run with {} walkers and {} steps'.format(
nwalkers, steps)
print "Mean acor time: " + str(np.mean(sampler.acor))
print "Mean acceptance fraction: " + str(
np.mean(sampler.acceptance_fraction))
print '\nRun took %r minutes' % ((stop - start) / 60.)
chain = sampler.chain
chi = (sampler.lnprobability) / (-0.5)
whatbywhat = str(nwalkers) + 'x' + str(steps)
os.system('mkdir MCMCRUNS/vis_and_sed/' + whatbywhat)
chainFile = 'MCMCRUNS/vis_and_sed/' + whatbywhat + '/' + whatbywhat + '.chain.fits'
chiFile = 'MCMCRUNS/vis_and_sed/' + whatbywhat + '/' + whatbywhat + '.chi.fits'
infoFile = 'MCMCRUNS/vis_and_sed/' + whatbywhat + '/' + whatbywhat + '.runInfo.txt'
fits.writeto(chainFile, chain)
fits.writeto(chiFile, chi)
#f = open('runInfo.txt','w')
f = open(infoFile, 'w')
f.write('run took %r minutes\n' % ((stop - start) / 60.))
f.write('walkers: %r\n' % nwalkers)
f.write('steps: %r\n' % steps)
f.write('initial model: %r\n' % p0)
f.write('widths: %r\n' % widths)
f.write("mean acor time: " + str(np.mean(sampler.acor)))
f.write("\nmean acceptance fraction: " +
str(np.mean(sampler.acceptance_fraction)))
f.close()
print 'Data written to: \n' + chainFile + '\n' + chiFile + '\n' + infoFile
def run_mcmc(self, n_walkers=100, n_iterations=100):
"""
Run emcee MCMC.
Args:
n_walkers (int): Number of walkers to pass to the MCMC.
n_iteratins (int): Number of iterations to pass to the MCMC.
"""
# Initialize walker matrix with initial parameters
walkers_matrix = [] # must be a list, not an np.array
for walker in range(n_walkers):
walker_params = []
for component in self.components:
walker_params = walker_params + component.initial_values(
self.data_spectrum)
walkers_matrix.append(walker_params)
global iteration_count
iteration_count = 0
# Create MCMC sampler. To enable multiproccessing, set threads > 1.
# If using multiprocessing, the "lnpostfn" and "args" parameters
# must be pickleable.
if self.mpi:
# Initialize the multiprocessing pool object.
from emcee.utils import MPIPool
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
self.sampler = emcee.EnsembleSampler(
nwalkers=n_walkers,
dim=len(walkers_matrix[0]),
lnpostfn=ln_posterior,
args=[self],
pool=pool,
runtime_sortingfn=sort_on_runtime)
self.sampler.run_mcmc(walkers_matrix, n_iterations)
pool.close()
else:
self.sampler = emcee.EnsembleSampler(nwalkers=n_walkers,
dim=len(walkers_matrix[0]),
lnpostfn=ln_posterior,
args=[self],
threads=1)
#self.sampler_output = self.sampler.run_mcmc(walkers_matrix, n_iterations)
self.sampler.run_mcmc(walkers_matrix, n_iterations)
def main():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--mpi', action='store_true', default=False)
parser.add_argument('--walkers', type=int, default=100)
parser.add_argument('--steps', type=int, default=1000)
opt = parser.parse_args()
pool = None
if opt.mpi:
import socket
import os
from emcee.utils import MPIPool
pool = MPIPool()
print('Running in MPI. Host', socket.gethostname(), 'pid',
os.getpid(), 'is master?', pool.is_master())
if not pool.is_master():
pool.wait()
return
ndim, nwalkers = 2, opt.walkers
ivar = 1. / np.random.rand(ndim)
p0 = [np.random.rand(ndim) for i in range(nwalkers)]
sampler = emcee.EnsembleSampler(nwalkers,
ndim,
lnprob,
args=[ivar],
pool=pool)
import time
print('Running for', opt.steps, 'steps with', opt.walkers, 'walkers')
t0 = time.time()
sampler.run_mcmc(p0, opt.steps)
print('Finished in', time.time() - t0, 'seconds')
if pool:
pool.close()
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
plt.figure()
for i in range(ndim):
plt.subplot(1, ndim, 1 + i)
plt.hist(sampler.flatchain[:, i], 100, color="k", histtype="step")
plt.title("Dimension {0:d}".format(i))
plt.savefig('plot.png')
print('Saved plot')
def fit_bim_bh3_curves(p0=None):
# Choose initial position
if p0 is None:
p0 = np.zeros((nwalkers, ndim))
for walk_ix in range(nwalkers):
for d_ix in range(len(data)):
p0[walk_ix, d_ix*3] = np.random.uniform(1, 6)
p0[walk_ix, d_ix*3 + 1] = np.random.uniform(6e-5, 1e-3)
p0[walk_ix, d_ix*3 + 2] = np.random.uniform(2, 3)
hp_ix = len(data)*3
p0[walk_ix, hp_ix] = np.random.uniform(1,6) # fmax mean
p0[walk_ix, hp_ix + 1] = np.random.uniform(0,1) # fmax sd
p0[walk_ix, hp_ix + 2] = np.random.uniform(6e-5, 1e-3) # k mean
p0[walk_ix, hp_ix + 3] = np.random.uniform(0,1e-1) # k sd
p0[walk_ix, hp_ix + 4] = np.random.uniform(2,3) # f0 mean
p0[walk_ix, hp_ix + 5] = np.random.uniform(0,1) # f0 sd
#plt.figure()
#for d_ix, data_i in enumerate(data):
# plt.plot(time, data_i, color=colors[d_ix])
# plt.plot(time, fit_func(p0[0, d_ix*3:(d_ix+1)*3]), color='k')
# Initialize the MPI pool
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
# Get the sampler
sampler = emcee.EnsembleSampler(nwalkers, ndim, posterior, pool=pool)
# Burn-in
print("Burn-in sampling...")
pos, prob, state = sampler.run_mcmc(p0, burn_steps, storechain=False)
sampler.reset()
# Main sampling
print("Main sampling...")
sampler.run_mcmc(pos, sample_steps)
# Close the pool!
pool.close()
# Pickle the sampler
sampler.pool = None
with open('bimbh3_141125_2.pck','w') as f:
pickle.dump(sampler, f)
return sampler
def run_pool(pC, pW, walk, step): #pCenter and pWidths
steps = step
nwalkers = walk
ndim = len(pC)
## r in, del r, i, PA
p0 = [pC[0], pC[1], pC[2], pC[3], pC[4]]
widths = [pW[0], pW[1], pW[2], pW[3], pW[4]]
p = emcee.utils.sample_ball(p0,widths,size=nwalkers)
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnlike_visonly, live_dangerously=True, pool=pool)
print 'Beginning the MCMC run.'
start = time.clock()
sampler.run_mcmc(p, steps)
stop = time.clock()
pool.close()
print 'MCMC finished successfully.\n'
print 'This was a visibility-only run with {} walkers and {} steps'.format(nwalkers,steps)
print "Mean acor time: "+str(np.mean(sampler.acor))
print "\nMean acceptance fraction: "+str(np.mean(sampler.acceptance_fraction))
print 'Run took %r minutes' % ((stop - start)/60.)
chain = sampler.chain
chi = (sampler.lnprobability)/(-0.5)
whatbywhat = str(nwalkers)+'x'+str(steps)
os.system('mkdir MCMCRUNS/vis_only/'+whatbywhat)
chainFile = 'MCMCRUNS/vis_only/'+whatbywhat+'/'+whatbywhat+'.chain.fits'
chiFile = 'MCMCRUNS/vis_only/'+whatbywhat+'/'+whatbywhat+'.chi.fits'
infoFile = 'MCMCRUNS/vis_only/'+whatbywhat+'/'+whatbywhat+'.runInfo.txt'
fits.writeto(chainFile,chain)
fits.writeto(chiFile,chi)
f = open(infoFile,'w')
f.write('run took %r minutes\n' % ((stop - start)/60.))
f.write('walkers: %r\n' % nwalkers)
f.write('steps: %r\n' % steps)
f.write('initial model: %r\n' % p0)
f.write('widths: %r\n' % widths)
f.write("mean acor time: "+str(np.mean(sampler.acor)))
f.write("\nmean acceptance fraction: "+str(np.mean(sampler.acceptance_fraction)))
f.close()
print 'Data written to: \n'+chainFile+'\n'+chiFile+'\n'+infoFile
def tdelay_dt_mcmc(run, theta, Niter=20, Nwalkers=10, Ndim=2, sigma_smhm=0.2, nsnap0=15, downsampled='14', flag=None, continue_chain=False):
'''
'''
if Ndim == 2:
tdelay_range = [0., 3.]#np.arange(0., 3., 0.5)
dt_range = [0.1, 4.]
# new chain
chain_file = ''.join([UT.fig_dir(), run, '.tdelay_dt_mcmc.chain.dat'])
if os.path.isfile(chain_file) and continue_chain:
print 'Continuing previous MCMC chain!'
sample = np.loadtxt(chain_file)
Niter = Niter - (np.float(len(sample))/np.float(Nwalkers)) # Number of chains left to finish
if Niter <= 0:
raise ValueError
print Niter, ' iterations left to finish'
else:
f = open(chain_file, 'w')
f.close()
# Initializing Walkers
pos0 = [np.array([np.random.uniform(tdelay_range[0], tdelay_range[1]), np.random.uniform(dt_range[0], dt_range[1])]) for i in range(Nwalkers)]
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
# Initializing the emcee sampler
kwargs = {
'theta': theta,
'sigma_smhm': 0.2,
'nsnap0': 15,
'downsampled': '14',
}
sampler = emcee.EnsembleSampler(Nwalkers, Ndim, sigM, pool=pool, kwargs=kwargs)
for result in sampler.sample(pos0, iterations=Niter, storechain=False):
position = result[0]
#print position
f = open(chain_file, 'a')
for k in range(position.shape[0]):
output_str = '\t'.join(position[k].astype('str')) + '\n'
f.write(output_str)
f.close()
pool.close()
return None
def lnPost(theta):
'''log-posterior
'''
# prior calculations
if prior_min[0] < theta[0] < prior_max[0] and \
prior_min[1] < theta[1] < prior_max[1] and \
prior_min[2] < theta[2] < prior_max[2] and \
prior_min[3] < theta[3] < prior_max[3] and \
prior_min[4] < theta[4] < prior_max[4]:
lnPrior = 0.0
else:
lnPrior = -np.inf
if not np.isfinite(lnPrior):
return -np.inf
return lnPrior + lnLike(theta)
"""Initializing Walkers"""
pos = [np.array([11. , np.log(.4) , 11.5 , 1.0 , 13.5]) + 1e-3*np.random.randn(Ndim) for i in range(Nwalkers)]
"""Initializing MPIPool"""
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
"""Initializing the emcee sampler"""
sampler = emcee.EnsembleSampler(Nwalkers, Ndim, lnprob, pool=pool)
# Burn in + Production
sampler.run_mcmc(pos, Nchains_burn + Nchains_pro)
# Production.
samples = sampler.chain[:, Nchains_burn:, :].reshape((-1, Ndim))
#closing the pool
pool.close()
np.savetxt("mcmc_sample.dat" , samples)
def main():
'''
A parallel run.
'''
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
clf = hbsgc.HBSGC(pool=pool)
# save start time
clf.last_clock = time.clock()
clf.filter_calcs()
clf.data_calcs()
clf.star_model_calcs()
# if clf.calc_model_mags:
# clf.star_model_mags()
clf.gal_model_calcs()
# if clf.calc_model_mags:
# clf.gal_model_mags()
clf.fit_calcs()
clf.count_tot = 0
clf.sample()
clf.save_proba()
if clf.min_chi2_write:
clf.save_min_chi2()
pool.close()
def main():
'''
A parallel run.
'''
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
clf = hbsgc.HBSGC(pool=pool)
# save start time
clf.last_clock = time.clock()
clf.filter_calcs()
clf.data_calcs()
clf.star_model_calcs()
# if clf.calc_model_mags:
# clf.star_model_mags()
clf.gal_model_calcs()
# if clf.calc_model_mags:
# clf.gal_model_mags()
clf.fit_calcs()
clf.count_tot = 0
clf.sample()
clf.save_proba()
if clf.min_chi2_write:
clf.save_min_chi2()
pool.close()
def lnPost(theta):
'''log-posterior
'''
# prior calculations
if prior_min[0] < theta[0] < prior_max[0] and \
prior_min[1] < theta[1] < prior_max[1] and \
prior_min[2] < theta[2] < prior_max[2] and \
prior_min[3] < theta[3] < prior_max[3] and \
prior_min[4] < theta[4] < prior_max[4]:
lnPrior = 0.0
else:
lnPrior = -np.inf
if not np.isfinite(lnPrior):
return -np.inf
return lnPrior + lnLike(theta)
"""Initializing Walkers"""
pos = [
np.array([11., np.log(.4), 11.5, 1.0, 13.5]) +
1e-3 * np.random.randn(Ndim) for i in range(Nwalkers)
]
"""Initializing MPIPool"""
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
"""Initializing the emcee sampler"""
sampler = emcee.EnsembleSampler(Nwalkers, Ndim, lnprob, pool=pool)
# Burn in + Production
sampler.run_mcmc(pos, Nchains_burn + Nchains_pro)
# Production.
samples = sampler.chain[:, Nchains_burn:, :].reshape((-1, Ndim))
#closing the pool
pool.close()
np.savetxt("mcmc_sample.dat", samples)
def ens_mpi_sample(gf, nwalkers, burn_steps, sample_steps, pos=None,
random_state=None):
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
# Initialize the parameter array with initial values (in log10 units)
# Number of parameters to estimate
ndim = (len(gf.builder.global_params) +
(len(gf.data) * len(gf.builder.local_params)))
# Initialize the walkers with starting positions drawn from the priors
# Note that the priors are in log10 scale already, so they don't
# need to be transformed here
if pos is None:
p0 = np.zeros((nwalkers, ndim))
for walk_ix in range(nwalkers):
for p_ix in range(ndim):
p0[walk_ix, p_ix] = gf.priors[p_ix].random()
else:
p0 = pos
# Create the sampler object
sampler = emcee.EnsembleSampler(nwalkers, ndim, posterior,
args=[gf], pool=pool)
if random_state is not None:
sampler.random_state = random_state
print "Burn in sampling..."
pos, prob, state = sampler.run_mcmc(p0, burn_steps, storechain=False)
sampler.reset()
print "Main sampling..."
sampler.run_mcmc(pos, sample_steps)
# Close the pool!
pool.close()
print "Done sampling."
return sampler
def runModel():
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
# pool=None
observation = simulateData()
nTrans = len(observation["spectype"])
ndim, nwalkers = 8 + nTrans, 1000
# mns = numpy.concatenate(([inputs.Om0, inputs.w0, inputs.rate_II_r, inputs.logL_snIa, inputs.sigma_snIa, \
# inputs.logL_snII,inputs.sigma_snII,inputs.Z], -.35*numpy.zeros(nTrans)))
sigs = numpy.concatenate(
(
[
0.1,
0.2,
0.1,
uncertainties.logL_snIa,
uncertainties.sigma_snIa,
uncertainties.logL_snII,
uncertainties.sigma_snII,
uncertainties.Z,
],
0.05 + numpy.zeros(nTrans),
)
)
p0 = []
for i in range(nwalkers):
dum = numpy.random.rand(nTrans)
dum = numpy.array(numpy.round(dum), dtype="int")
lnL_init = dum + (1 - dum) * 0.5
lnL_init = numpy.log(lnL_init)
mns = numpy.concatenate(
(
[
inputs.Om0,
inputs.w0,
inputs.rate_II_r,
inputs.logL_snIa,
inputs.sigma_snIa,
inputs.logL_snII,
inputs.sigma_snII,
inputs.Z,
],
lnL_init,
)
)
p0.append((numpy.random.rand(ndim) - 0.5) * sigs + mns)
# p0 = [numpy.random.randn(ndim)*sigs + mns for i in range(nwalkers)]
dco = 1e-11 # measurement error very small
sampler = emcee.EnsembleSampler(
nwalkers,
ndim,
lnprob,
args=[
observation["counts"],
observation["specz"],
numpy.zeros(nTrans) + dco,
observation["zprob"],
observation["spectype"],
],
pool=pool,
)
sampler.run_mcmc(p0, 2000)
pool.close()
output = open("data.pkl", "wb")
pickle.dump(sampler.chain, output)
output.close()
class MPIManager(object):
"""
Class to serve as context manager to handle to MPI-related issues,
specifically, the managing of ``MPIPool`` and splitting of communicators
"""
logger = logging.getLogger("MPIManager")
def __init__(self, comm, nruns, debug=False):
"""
Parameters
----------
comm : MPI.Communicator
the global communicator to split
nruns : int
the number of independent algorithms to run concurrently
debug : bool, optional
set the logging level to debug in the `MPIPool`; default
is `False`
"""
self.comm = comm
self.nruns = nruns
self.debug = debug
if debug: self.logger.setLevel(logging.DEBUG)
# initialize comm for parallel runs
self.par_runs_group = None
self.par_runs_comm = None
# intiialize comm for pool of workers for each
# parallel run
self.pool_comm = None
self.pool = None
def __enter__(self):
"""
Setup the MPIPool, such that only the ``pool`` master returns,
while the other processes wait for tasks
"""
# split ranks if we need to
if self.comm.size > 1:
ranges = []
for i, ranks in split_ranks(self.comm.size, self.nruns):
ranges.append(ranks[0])
if self.comm.rank in ranks: color = i
# split the global comm into pools of workers
self.pool_comm = self.comm.Split(color, 0)
# make the comm to communicate b/w parallel runs
if self.nruns > 1:
self.par_runs_group = self.comm.group.Incl(ranges)
self.par_runs_comm = self.comm.Create(self.par_runs_group)
# initialize the MPI pool, if the comm has more than 1 process
if self.pool_comm is not None and self.pool_comm.size > 1:
from emcee.utils import MPIPool
kws = {
'loadbalance': True,
'comm': self.pool_comm,
'debug': self.debug
}
self.pool = MPIPool(**kws)
# explicitly force non-master ranks in pool to wait
if self.pool is not None and not self.pool.is_master():
self.pool.wait()
self.logger.debug("exiting after pool closed")
sys.exit(0)
# log
if self.pool is not None:
self.logger.debug("using an MPIPool instance with %d worker(s)" %
self.pool.size)
self.rank = 0
if self.par_runs_comm is not None:
self.rank = self.par_runs_comm.rank
return self
def __exit__(self, exc_type, exc_value, exc_traceback):
"""
Exit gracefully by closing and freeing the MPI-related variables
"""
if exc_value is not None:
trace = ''.join(
traceback.format_exception(exc_type,
exc_value,
exc_traceback,
limit=5))
self.logger.error("traceback:\n%s" % trace)
# wait for all the processes, if we more than one
if self.par_runs_comm is not None and self.par_runs_comm.size > 1:
self.par_runs_comm.Barrier()
# close and free the MPI stuff
self.logger.debug("beginning to close MPI variables...")
if self.par_runs_group is not None:
self.par_runs_group.Free()
if self.par_runs_comm is not None:
self.par_runs_comm.Free()
if self.pool is not None:
self.pool.close()
self.logger.debug('...MPI variables closed')
return True
def main():
#################################################
############Option parsing#######################
#################################################
#Parse command line options
parser = argparse.ArgumentParser()
parser.add_argument("-f","--file",dest="options_file",action="store",type=str,help="analysis options file")
parser.add_argument("-v","--verbose",dest="verbose",action="store_true",default=False,help="turn on verbosity")
parser.add_argument("-vv","--verbose_plus",dest="verbose_plus",action="store_true",default=False,help="turn on additional verbosity")
parser.add_argument("-m","--mask_scale",dest="mask_scale",action="store_true",default=False,help="scale peaks and power spectrum to unmasked area")
parser.add_argument("-c","--cut_convergence",dest="cut_convergence",action="store",default=None,help="select convergence values in (min,max) to compute the likelihood. Safe for single descriptor only!!")
parser.add_argument("-g","--group_subfields",dest="group_subfields",action="store_true",default=False,help="group feature realizations by taking the mean over subfields, this makes a big difference in the covariance matrix")
parser.add_argument("-s","--save_features",dest="save_features",action="store_true",default=False,help="save features profiles")
parser.add_argument("-ss","--save",dest="save",action="store_true",default=False,help="save the best fits and corresponding chi2")
parser.add_argument("-p","--prefix",dest="prefix",action="store",default="",help="prefix of the emulator to pickle")
parser.add_argument("-l","--likelihood",dest="likelihood",action="store_true",default=False,help="save the likelihood cubes for the mocks")
parser.add_argument("-o","--observation",dest="observation",action="store_true",default=False,help="append the actual observation results to the mock results for direct comparison")
parser.add_argument("-d","--differentiate",dest="differentiate",action="store_true",default=False,help="differentiate the first minkowski functional to get the PDF")
cmd_args = parser.parse_args()
if cmd_args.options_file is None:
parser.print_help()
sys.exit(0)
#Set verbosity level
if cmd_args.verbose_plus:
logging.basicConfig(level=DEBUG_PLUS)
elif cmd_args.verbose:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
#Initialize MPI Pool
try:
pool = MPIPool()
except:
pool = None
if (pool is not None) and (not pool.is_master()):
pool.wait()
sys.exit(0)
if pool is not None:
logging.info("Started MPI Pool.")
#################################################################################################################
#################Info gathering: covariance matrix, observation and emulator#####################################
#################################################################################################################
#start
start = time.time()
last_timestamp = start
#Instantiate a FeatureLoader object that will take care of the memory loading
feature_loader = FeatureLoader(cmd_args)
###########################################################################################################################################
#Use this model for the covariance matrix (from the new set of 50 N body simulations)
covariance_model = CFHTcov.getModels(root_path=feature_loader.options.get("simulations","root_path"))
logging.info("Measuring covariance matrix from model {0}".format(covariance_model))
#Load in the covariance matrix
fiducial_feature_ensemble = feature_loader.load_features(covariance_model)
fiducial_features = fiducial_feature_ensemble.mean()
features_covariance = fiducial_feature_ensemble.covariance()
#timestamp
now = time.time()
logging.info("covariance loaded in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
################################################################################################################################################
#Treat the 50N-body simulation set as data
observation = CFHTcov.getModels(root_path=feature_loader.options.get("observations","root_path"))
logging.info("Measuring the observations from {0}".format(observation))
#And load the observations
observed_feature = feature_loader.load_features(observation)
#timestamp
now = time.time()
logging.info("observation loaded in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
################################################################################################################################################
#Create a LikelihoodAnalysis instance by unpickling one of the emulators
emulators_dir = os.path.join(feature_loader.options.get("analysis","save_path"),"emulators")
emulator_file = os.path.join(emulators_dir,"emulator{0}_{1}.p".format(cmd_args.prefix,output_string(feature_loader.feature_string)))
logging.info("Unpickling emulator from {0}...".format(emulator_file))
analysis = LikelihoodAnalysis.load(emulator_file)
#timestamp
now = time.time()
logging.info("emulator unpickled in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
####################################################################################################################
######################################Compute the chi2 cube#########################################################
####################################################################################################################
logging.info("Initializing chi2 meshgrid...")
#Set the points in parameter space on which to compute the chi2 (read from options)
Om = np.ogrid[feature_loader.options.getfloat("Omega_m","min"):feature_loader.options.getfloat("Omega_m","max"):feature_loader.options.getint("Omega_m","num_points")*1j]
w = np.ogrid[feature_loader.options.getfloat("w","min"):feature_loader.options.getfloat("w","max"):feature_loader.options.getint("w","num_points")*1j]
si8 = np.ogrid[feature_loader.options.getfloat("sigma8","min"):feature_loader.options.getfloat("sigma8","max"):feature_loader.options.getint("sigma8","num_points")*1j]
num_points = len(Om) * len(w) * len(si8)
points = np.array(np.meshgrid(Om,w,si8,indexing="ij")).reshape(3,num_points).transpose()
#Now compute the chi2 at each of these points
if pool:
split_chunks = pool.size
logging.info("Computing chi squared for {0} parameter combinations using {1} cores...".format(points.shape[0],pool.size))
else:
split_chunks = None
logging.info("Computing chi squared for {0} parameter combinations using 1 core...".format(points.shape[0]))
#Allocate array for best fit
first_realization = feature_loader.options.getint("mocks","first_realization")
last_realization = feature_loader.options.getint("mocks","last_realization")
if cmd_args.observation:
best_fit_all = np.zeros((last_realization-first_realization+1 + 1,analysis.parameter_set.shape[1]))
chi2_all = np.zeros(last_realization-first_realization+1 + 1)
chi2_from_expected_all = np.zeros(last_realization-first_realization+1 + 1)
else:
best_fit_all = np.zeros((last_realization-first_realization+1,analysis.parameter_set.shape[1]))
chi2_all = np.zeros(last_realization-first_realization+1)
chi2_from_expected_all = np.zeros(last_realization-first_realization+1)
#Cycle through the realizations and obtain a best fit for each one of them
for nreal in range(first_realization-1,last_realization):
chi_squared = analysis.chi2(points,observed_feature=observed_feature[nreal],features_covariance=features_covariance,pool=pool,split_chunks=split_chunks)
now = time.time()
logging.info("realization {0}, chi2 calculations completed in {1:.1f}s".format(nreal+1,now-last_timestamp))
last_timestamp = now
#After chi2, compute the likelihood
likelihood_cube = analysis.likelihood(chi_squared.reshape(Om.shape + w.shape + si8.shape))
#Maybe save the likelihood cube?
if cmd_args.likelihood:
likelihood_filename = os.path.join(feature_loader.options.get("analysis","save_path"),"troubleshoot","likelihood{0}_{1}.npy".format(nreal+1,output_string(feature_loader.feature_string)))
logging.info("Saving likelihood cube to {0}...".format(likelihood_filename))
np.save(likelihood_filename,likelihood_cube)
#Maybe save the feature profiles?
if cmd_args.save_features:
features_filename = os.path.join(feature_loader.options.get("analysis","save_path"),"troubleshoot","features{0}_{1}.npy".format(nreal+1,output_string(feature_loader.feature_string)))
logging.info("Saving features for realization {0} to {1}...".format(nreal+1,features_filename))
np.save(features_filename,observed_feature[nreal])
#Find the maximum of the likelihood using ContourPlot functionality
contour = ContourPlot()
contour.getLikelihood(likelihood_cube)
contour.getUnitsFromOptions(feature_loader.options)
parameters_maximum = contour.getMaximum()
parameter_keys = parameters_maximum.keys()
parameter_keys.sort(key=contour.parameter_axes.get)
#Display the new best fit before exiting
best_fit_parameters = np.array([ parameters_maximum[par_key] for par_key in parameter_keys ])
best_fit_chi2 = analysis.chi2(best_fit_parameters,features_covariance=features_covariance,observed_feature=observed_feature[nreal])[0]
chi2_from_expected = analysis.chi2(np.array([0.26,-1.0,0.800]),features_covariance=features_covariance,observed_feature=observed_feature[nreal])[0]
logging.info("Best fit for realization {4} is [ {0[0]:.2f} {0[1]:.2f} {0[2]:.2f} ], chi2_best={1:.3f}({2} dof), chi2_expected={3:.3f}({2} dof)".format(best_fit_parameters,best_fit_chi2,analysis.training_set.shape[1],chi2_from_expected,nreal+1))
#Update global array with best fit parameters and corresponding chi2
best_fit_all[nreal-first_realization+1,:] = best_fit_parameters.copy()
chi2_all[nreal-first_realization+1] = best_fit_chi2
chi2_from_expected_all[nreal-first_realization+1] = chi2_from_expected
#######################################################################################################################################################################
#If option was selected, append the observation results to the mock ones, for comparison
if cmd_args.observation:
observed_feature = feature_loader.load_features(CFHTLens(root_path=feature_loader.options.get("observations","root_path")))[0]
chi_squared = analysis.chi2(points,observed_feature=observed_feature,features_covariance=features_covariance,pool=pool,split_chunks=split_chunks)
now = time.time()
logging.info("actual observation, chi2 calculations completed in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
#After chi2, compute the likelihood
likelihood_cube = analysis.likelihood(chi_squared.reshape(Om.shape + w.shape + si8.shape))
#Maybe save the likelihood cube?
if cmd_args.likelihood:
likelihood_filename = os.path.join(feature_loader.options.get("analysis","save_path"),"troubleshoot","likelihood_obs_{0}.npy".format(output_string(feature_loader.feature_string)))
logging.info("Saving likelihood cube to {0}...".format(likelihood_filename))
np.save(likelihood_filename,likelihood_cube)
#Maybe save the feature profiles?
if cmd_args.save_features:
features_filename = os.path.join(feature_loader.options.get("analysis","save_path"),"troubleshoot","features_obs_{0}.npy".format(output_string(feature_loader.feature_string)))
logging.info("Saving observed features to {0}...".format(features_filename))
np.save(features_filename,observed_feature)
#Find the maximum of the likelihood using ContourPlot functionality
contour = ContourPlot()
contour.getLikelihood(likelihood_cube)
contour.getUnitsFromOptions(feature_loader.options)
parameters_maximum = contour.getMaximum()
parameter_keys = parameters_maximum.keys()
parameter_keys.sort(key=contour.parameter_axes.get)
#Display the new best fit before exiting
best_fit_parameters = np.array([ parameters_maximum[par_key] for par_key in parameter_keys ])
best_fit_chi2 = analysis.chi2(best_fit_parameters,features_covariance=features_covariance,observed_feature=observed_feature)[0]
chi2_from_expected = analysis.chi2(np.array([0.26,-1.0,0.800]),features_covariance=features_covariance,observed_feature=observed_feature)[0]
logging.info("Best fit for observation is [ {0[0]:.2f} {0[1]:.2f} {0[2]:.2f} ], chi2_best={1:.3f}({2} dof), chi2_expected={3:.3f}({2} dof)".format(best_fit_parameters,best_fit_chi2,analysis.training_set.shape[1],chi2_from_expected))
#Update global array with best fit parameters and corresponding chi2
best_fit_all[-1,:] = best_fit_parameters.copy()
chi2_all[-1] = best_fit_chi2
chi2_from_expected_all[-1] = chi2_from_expected
#######################################################################################################################################################################
#Close MPI Pool
if pool is not None:
pool.close()
logging.info("Closed MPI Pool.")
if cmd_args.save:
#Save the best fit parameters for all realizations
best_fit_filename = os.path.join(feature_loader.options.get("analysis","save_path"),"troubleshoot","best_fit_all_{0}.npy".format(output_string(feature_loader.feature_string)))
logging.info("Saving best fit to {0}...".format(best_fit_filename))
np.save(best_fit_filename,best_fit_all)
#Save the best fit chi2 for all realizations
chi2_filename = os.path.join(feature_loader.options.get("analysis","save_path"),"troubleshoot","chi2_all_{0}.npy".format(output_string(feature_loader.feature_string)))
logging.info("Saving best fit chi2 to {0}...".format(chi2_filename))
np.save(chi2_filename,chi2_all)
#Save also the chi2 for the expected best fit
chi2_filename = os.path.join(feature_loader.options.get("analysis","save_path"),"troubleshoot","chi2_all_expected_{0}.npy".format(output_string(feature_loader.feature_string)))
logging.info("Saving expected chi2 to {0}...".format(chi2_filename))
np.save(chi2_filename,chi2_from_expected_all)
end = time.time()
logging.info("DONE!!")
logging.info("Completed in {0:.1f}s".format(end-start))
def main():
# firstly, read one file and get k bins we want for the fitting range; It's dark matter power spectrum in redshift space
parameter_file = sys.argv[1]
with open(parameter_file, 'r') as fr:
input_params = yaml.load(fr)
data_m = np.genfromtxt(
input_params['Pwig_ifile'],
dtype='f8',
comments='#',
delimiter='',
skip_header=11
) # skip the first data row, the first 10 rows are comments.
#print(data_m)
num_kbin = np.size(data_m, axis=0)
kk = data_m[:, 0]
# get indices based on the ascending k
indices_sort = [i[0] for i in sorted(enumerate(kk), key=lambda x: x[1])]
# sort out the indices whose k<=0.3 h/Mpc
for i in range(num_kbin):
if kk[indices_sort[i]] > 0.3:
break
print(indices_sort[i - 1])
indices_p = indices_sort[0:i]
k_p = kk[indices_p]
N_fitbin = len(k_p)
mu_p, Pwig = data_m[indices_p, 1], data_m[indices_p, 2]
print(k_p, N_fitbin)
# input Pnow, note the (k, mu) indices have the same order as those of Pwig data file
data_m = np.genfromtxt(input_params['Pnow_ifile'],
dtype='f8',
comments='#',
delimiter='',
skip_header=11)
Pnow = data_m[indices_p, 2]
Pwnw_diff_obs = Pwig - Pnow
# input diagonal terms of covariance matrix of (Pwig-Pnow)
diag_Cov_Pwnw = np.loadtxt(input_params['diag_Cov_Pwnw_ifile'],
dtype='f8',
comments='#',
usecols=(2, ))
ivar_Pk_wnow = 1.0 / diag_Cov_Pwnw
#print(ivar_Pk_wnow)
# input (theoretical) linear power spectrum
k_wiggle, Pk_wiggle = np.loadtxt(input_params['Pwig_linear'],
dtype='f8',
comments='#',
unpack=True)
tck_Pk_linw = interpolate.splrep(k_wiggle, Pk_wiggle)
k_smooth, Pk_smooth = np.loadtxt(input_params['Pnow_linear'],
dtype='f8',
comments='#',
unpack=True)
tck_Pk_sm = interpolate.splrep(k_smooth, Pk_smooth)
q_max = 110.0 # Mpc/h, BAO radius
Sigma2_sm_array = np.linspace(10.0, 610.0, 61)
#print(Sigma2_sm_array)
#const = 1.0
Sigma2_dd_array = np.array([
integrate.quad(Sigma2_dd_integrand,
1.05e-5,
100.0,
args=(tck_Pk_linw, q_max, Sigma2_sm),
epsabs=1.e-4,
epsrel=1.e-4)[0] for Sigma2_sm in Sigma2_sm_array
])
Sigma2_sd_array = np.array([
integrate.quad(Sigma2_sd_integrand,
1.05e-5,
100.0,
args=(tck_Pk_linw, q_max, Sigma2_sm),
epsabs=1.e-4,
epsrel=1.e-4)[0] for Sigma2_sm in Sigma2_sm_array
])
Sigma2_ss_array = np.array([
integrate.quad(Sigma2_ss_integrand,
1.05e-5,
100.0,
args=(tck_Pk_linw, q_max, Sigma2_sm),
epsabs=1.e-4,
epsrel=1.e-4)[0] for Sigma2_sm in Sigma2_sm_array
])
tck_Sigma2_dd = interpolate.splrep(Sigma2_sm_array, Sigma2_dd_array, k=3)
tck_Sigma2_sd = interpolate.splrep(Sigma2_sm_array, Sigma2_sd_array, k=3)
tck_Sigma2_ss = interpolate.splrep(Sigma2_sm_array, Sigma2_ss_array, k=3)
all_params = list(input_params['init_params'].values())
params_indices = input_params['params_indices']
params_name = list(input_params['init_params'].keys())
all_temperature = input_params['all_temperature']
N_params, theta, fix_params, params_T, params_name = set_params(
all_params, params_indices, params_name, all_temperature)
print(N_params, theta, fix_params, params_T, params_name)
sim_z = input_params['sim_z'] # redshift of the simulated power spectrum
N_walkers = input_params['N_walkers']
Omega_m = input_params['Omega_m']
G_0 = growth_factor(0.0, Omega_m) # G_0 at z=0, normalization factor
norm_gf = growth_factor(sim_z, Omega_m) / G_0
const = 1.0 / (6.0 * np.pi**2.0) * norm_gf**2.0
pool = MPIPool(loadbalance=True)
np.random.seed(1) # set random seed for random number generator
params_mcmc = mcmc_routine(N_params, N_walkers, theta, params_T,
params_indices, fix_params, k_p, mu_p,
Pwnw_diff_obs, ivar_Pk_wnow, tck_Pk_linw,
tck_Pk_sm, tck_Sigma2_dd, tck_Sigma2_sd,
tck_Sigma2_ss, norm_gf, const, params_name,
pool)
print(params_mcmc)
chi_square = chi2(params_mcmc[:, 0], params_indices, fix_params, k_p, mu_p,
Pwnw_diff_obs, ivar_Pk_wnow, tck_Pk_linw, tck_Pk_sm,
tck_Sigma2_dd, tck_Sigma2_sd, tck_Sigma2_ss, norm_gf,
const)
dof = N_fitbin - N_params
reduced_chi2 = chi_square / dof
odir = './output_files/'
if not os.path.exists(odir):
os.makedirs(odir)
ofile_params = odir + input_params['ofile_name'].format(
sim_z, ''.join(map(str, params_indices)))
write_params(ofile_params, params_mcmc, params_name, reduced_chi2,
fix_params, dof)
pool.close()
def mcmc(tag=None,
zbin=1,
nwalkers=48,
Nchains=4,
minlength=600,
likelihood='pseudo'):
'''
Parameters
----------
Nchains : int
Number of independent chains to run for the gelman rubin convergence test
'''
if tag is None:
raise ValueError("specify a tag, otherwise it's confusing")
temperature = 2.e-3 # temperature
# read in BOSS P(k) NGC
pkay = Dat.Pk()
k0, p0k_ngc = pkay.Observation(0, zbin, 'ngc')
k2, p2k_ngc = pkay.Observation(2, zbin, 'ngc')
k4, p4k_ngc = pkay.Observation(4, zbin, 'ngc')
pk_ngc_list = [p0k_ngc, p2k_ngc, p4k_ngc]
k_list = [k0, k2, k4]
# read in BOSS P(k) SGC
k0, p0k_sgc = pkay.Observation(0, zbin, 'sgc')
k2, p2k_sgc = pkay.Observation(2, zbin, 'sgc')
k4, p4k_sgc = pkay.Observation(4, zbin, 'sgc')
pk_sgc_list = [p0k_sgc, p2k_sgc, p4k_sgc]
if likelihood == 'psuedo': # standard pseudo Gaussian likelihood
# read in Covariance matrix
# currently for testing purposes,
# implemented to read in Florian's covariance matrix
_, _, C_pk_ngc = Dat.beutlerCov(zbin, NorS='ngc', ell='all')
_, _, C_pk_sgc = Dat.beutlerCov(zbin, NorS='sgc', ell='all')
# calculate precision matrices (including the hartlap factor)
Cinv_ngc = np.linalg.inv(C_pk_ngc)
Cinv_sgc = np.linalg.inv(C_pk_sgc)
# hartlap factor
n_mocks_ngc = 2045
n_mocks_sgc = 2048
f_hartlap_ngc = (float(n_mocks_ngc) - float(
len(np.concatenate(pk_ngc_list))) - 2.) / (float(n_mocks_ngc) - 1.)
f_hartlap_sgc = (float(n_mocks_sgc) - float(
len(np.concatenate(pk_sgc_list))) - 2.) / (float(n_mocks_sgc) - 1.)
Cinv_ngc *= f_hartlap_ngc
Cinv_sgc *= f_hartlap_sgc
# ln Posterior function
lnPost = lnPost_pseudo
# args for ln Posterior function
# data ks, BOSS NGC P_l(k), BOSS SGC P_l(k), NGC precision matrix, SGC precision matrix
lnpost_args = (k_list, pk_ngc_list, pk_sgc_list, Cinv_ngc, Cinv_sgc)
elif likelihood in ['pca', 'ica']:
# read in patchy mock P(k)s for ngc and sgc
pk_ngc_list, pk_sgc_list = [], []
for ell in [0, 2, 4]:
if ell == 4: kmax = 0.1
else: kmax = 0.15
pk_ngc_list.append(
NG.X_pk('patchy.z' + str(kwargs['zbin']),
krange=[0.01, kmax],
ell=ell,
NorS='ngc',
sys='fc'))
pk_sgc_list.append(
NG.X_pk('patchy.z' + str(kwargs['zbin']),
krange=[0.01, kmax],
ell=ell,
NorS='sgc',
sys='fc'))
pk_ngc_mock = np.concatenate(pk_ngc_list, axis=1)
pk_sgc_mock = np.concatenate(pk_sgc_list, axis=1)
else:
raise NotImplementedError
if zbin == 1: # 0.2 < z < 0.5
# maximum likelihood value
start = np.array([
1.008, 1.001, 0.478, 1.339, 1.337, 1.16, 0.32, -1580., -930., 6.1,
6.8
])
ndim = len(start)
# initialize MPI pool
try:
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
except ValueError:
pool = None
print("initializing ", Nchains, " independent emcee chains")
pos, samplers = [], []
for ichain in range(Nchains):
pos.append([
start + temperature * start *
(2. * np.random.random_sample(ndim) - 1.) for i in range(nwalkers)
])
samplers.append(
emcee.EnsembleSampler(nwalkers,
ndim,
lnPost,
args=lnpost_args,
pool=pool))
# Start MCMC
print("Running MCMC...")
withinchainvar = np.zeros((Nchains, ndim))
meanchain = np.zeros((Nchains, ndim))
scalereduction = np.repeat(2., ndim)
# bunch of numbers for the mcmc run
itercounter = 0
chainstep = minlength
loop = 1
epsilon = 0.02 #0.02
ichaincheck = 100
rstate = np.random.get_state()
while loop:
itercounter += chainstep
print("chain length =", itercounter)
for jj in range(Nchains):
for result in samplers[jj].sample(pos[jj],
iterations=chainstep,
rstate0=rstate,
storechain=True):
pos[jj] = result[0]
chainchi2 = -2. * result[1]
rstate = result[2]
# append chain outputs to chain file
chain_file = ''.join([
UT.dat_dir(), 'mcmc/', tag, '.chain',
str(jj), '.zbin',
str(zbin), '.dat'
])
f = open(chain_file, 'a')
for k in range(pos[jj].shape[0]):
output_str = '\t'.join(
pos[jj][k].astype('str')) + '\t' + str(
chainchi2[k]) + '\n'
f.write(output_str)
f.close()
# we do the convergence test on the second half of the current chain (itercounter/2)
chainsamples = samplers[jj].chain[:, itercounter / 2:, :].reshape(
(-1, ndim))
withinchainvar[jj] = np.var(chainsamples, axis=0)
meanchain[jj] = np.mean(chainsamples, axis=0)
scalereduction = gelman_rubin_convergence(withinchainvar, meanchain,
itercounter / 2, Nchains,
ndim)
print("scalereduction = ", scalereduction)
loop = 0
for jj in range(ndim):
if np.abs(1 - scalereduction[jj]) > epsilon:
loopcriteria = 1
chainstep = ichaincheck
if pool is not None:
pool.close()
return None
def fit_BAO(args):
kmin = float(args.kmin)
kmax = float(args.kmax)
params_str = args.params_str
Pk_type = args.Pk_type
params_indices = [int(i) for i in params_str]
old_stdout = sys.stdout
odir = './fit_kmin{}_kmax{}_{}/'.format(kmin, kmax, Pk_type)
if not os.path.exists(odir):
os.makedirs(odir)
ofile = odir + "mcmc_fit_params{}.log".format(params_str)
log_file = open(ofile, "w")
sys.stdout = log_file
print('Arguments for the fitting: ', args)
ifile = '/Users/mehdi/work/quicksurvey/ELG/run8/planck_camb_56106182_matterpower_z0.dat'
klin, Pk_linw = np.loadtxt(ifile, dtype='f8', comments='#', unpack=True)
Pwig_spl = InterpolatedUnivariateSpline(klin, Pk_linw)
ifile = '/Users/mehdi/work/quicksurvey/ELG/run8/planck_camb_56106182_matterpower_smooth_z0.dat'
klin, Pk_sm = np.loadtxt(ifile, dtype='f8', comments='#', unpack=True)
Psm_spl = InterpolatedUnivariateSpline(klin, Pk_sm)
norm_gf = 1.0
N_walkers = 40
##params_indices = [1, 0, 0] # 1: free parameter; 0: fixed parameter
all_param_names = 'alpha', 'Sigma2_xy', 'A', 'B'
all_temperature = 0.01, 1.0, 0.1, 0.1
Omega_m = 0.3075 # matter density
G_0 = growth_factor(0.0, Omega_m)
Sigma_0 = 7.7840 # This is exactly calculated from theoretical prediction with q_{BAO}=110 Mpc/h.
z_list = [0.625] #, 0.875, 1.125, 1.375] # z list for the data files
cut_list = ['F'] #, 'T']
# initial guess for fitting, Sigma2_xy=31.176 at z=0.65 is from theory prediction
alpha, A, B = 1.0, 1.0, 10.0
idir = '../kp0kp2knmodes/surveyscaled-nmodes/'
odir = './mcmc_fit_params_{}/kmin{}_kmax{}/'.format(Pk_type, kmin, kmax)
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
if rank == 0:
if not os.path.exists(odir):
os.makedirs(odir)
pool = MPIPool(loadbalance=True)
for z_value in z_list:
norm_gf = growth_factor(z_value, Omega_m) / G_0
Sigma2_xy = (Sigma_0 * norm_gf)**2.0
print('z, Sigma2_xy: ', z_value, Sigma2_xy)
all_params = alpha, Sigma2_xy, A, B
N_params, theta, fix_params, params_T, params_name = set_params(
all_params, params_indices, all_param_names, all_temperature)
for cut_type in cut_list:
ifile = idir + 'kp0kp2knmodes_z{}RADECcut{}.dat'.format(
z_value, cut_type)
print(ifile)
data_m = np.loadtxt(ifile, dtype='f8',
comments='#') # k, P0(k), P2(k), N_modes
indices = np.argwhere((data_m[:, 0] >= kmin)
& (data_m[:, 0] <= kmax)).flatten()
N_fitbin = len(indices)
k_obs, Pk_wig_obs, N_modes = data_m[indices,
0], data_m[indices,
1], data_m[indices,
3]
ivar_Pk_wig = N_modes / (2.0 * Pk_wig_obs**2.0)
#print('ivar_Pk_wig', ivar_Pk_wig)
params_mcmc = mcmc_routine(N_params, N_walkers, theta, params_T,
params_indices, fix_params, k_obs,
Pk_wig_obs, ivar_Pk_wig, Pwig_spl,
Psm_spl, norm_gf, params_name, pool)
print(params_mcmc)
chi_square = chi2(params_mcmc[:, 0], params_indices, fix_params,
k_obs, Pk_wig_obs, ivar_Pk_wig, Pwig_spl,
Psm_spl, norm_gf)
reduced_chi2 = chi_square / (N_fitbin - N_params)
print("chi^2/dof: ", reduced_chi2, "\n")
ofile_params = odir + 'fit_p0_z{}RADECcut{}_params{}.dat'.format(
z_value, cut_type, params_str)
write_params(ofile_params, params_mcmc, params_name, reduced_chi2)
pool.close()
sys.stdout = old_stdout
log_file.close()
def sample(self):
'''
Run the MCMC.
'''
# First make sure that the maximum likelihood params are fitted
if not self.minimized:
self.approximate_ml()
# print(self.params_all)
ndim, nwalkers = len(self.params_vary), self.config['NWALKERS']
p0 = np.zeros((nwalkers, len(self.params_vary)))
pml = [self.params_all[pname] for pname in self.params_vary]
for pnum, pname in enumerate(self.params_vary):
p0[:, pnum] = (np.random.randn(nwalkers)\
* self.config['SAMPLE_BALL']+1.)*pml[pnum]
plist = []
for key in self.params_vary.keys():
plist.append(key)
args = (self.freqs, self.tb_meas, self.var_tb, self.params_all, plist,
self.params_vary, self.fg_model, self.sig_model)
if self.config['MPI']:
from emcee.utils import MPIPool
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
self.sampler = emcee.EnsembleSampler(nwalkers,
ndim,
lnprob,
args=args,
pool=pool)
self.sampler.run_mcmc(p0, self.config['NBURN']) # burn in
p0 = self.sampler.chain[:, -1, :].squeeze()
self.sampler.reset()
self.sampler.run_mcmc(p0, self.config['NSTEPS'])
pool.close()
else:
if self.config['SAMPLER'] == 'PARALLELTEMPERING':
logl = lambda x: lnlike(
x, self.freqs, self.tb_meas, self.var_tb, self.params_all,
self.params_vary, self.fg_model, self.sig_model)
logp = lambda x: lnprior(x, self.params_vary.keys(), self.
params_vary)
self.sampler = ptemcee.Sampler(
ntemps=self.config['NTEMPS'],
nwalkers=self.config['NWALKERS'],
dim=self.ndim,
logl=logl,
logp=logp)
else:
self.sampler = emcee.EnsembleSampler(
nwalkers=self.config['NWALKERS'],
ndim=ndim,
log_prob_fn=lnprob,
args=args,
threads=self.config['THREADS'])
# If we use PT sampling, we need a further dimension of
# start parameters for the different temperatures
if self.config['SAMPLER'] == 'PARALLELTEMPERING':
p0 = np.array([p0 for m in range(self.config['NTEMPS'])])
# Run the MCMC for the burn-in
self.sampler.run_mcmc(p0,
self.config['NBURN'],
thin=self.config['NTHIN'])
# Reset after burn-in and run the full chain
if self.config['SAMPLER'] == 'PARALLELTEMPERING':
p0 = self.sampler.chain[:, :, -1, :]
else:
p0 = self.sampler.chain[:, -1, :].squeeze()
self.sampler.reset()
self.sampler.run_mcmc(p0,
self.config['NSTEPS'],
thin=self.config['NTHIN'])
# Create output directory
if not os.path.exists(self.config['PROJECT_NAME']):
os.makedirs(self.config['PROJECT_NAME'])
# Save output and configuration
with open(os.path.join(self.config['PROJECT_NAME'], 'config.yaml'),
'w') as f:
yaml.dump(self.config, f, default_flow_style=False)
with open(os.path.join(self.config['PROJECT_NAME'], 'ml_params.yaml'),
'w') as f:
yaml.dump(self.params_all, f, default_flow_style=False)
self.sampled = True
# Collect result parameters
###########################
resultdict = {}
# Chain
#######
resultdict['chain'] = self.sampler.chain,
# Conservative evidence
#######################
if (self.config['COMPUTECOVARIANCE'] &
(self.config['SAMPLER'] == 'ENSEMBLESAMPLER')):
# Estimate autocorrelation
self.acors = self.sampler.acor.astype(int)
resultdict['autocorrs'] = self.acors
# Estimate covariance
self.cov_samples = np.zeros(
(len(self.params_vary), len(self.params_vary)))
resultdict['cov_samples'] = self.cov_samples
for i in range(len(self.params_vary)):
for j in range(len(self.params_vary)):
stepsize = np.max([self.acors[i], self.acors[j]])
csample_i = self.sampler.chain[i, ::stepsize, :].flatten()
csample_j = self.sampler.chain[j, ::stepsize, :].flatten()
self.cov_samples[i, j] = np.mean(
(csample_i - csample_i.mean()) *
(csample_j - csample_j.mean()))
# Compute conservative evidence without prior factor
self.conservative_evidence = np.exp(self.ln_ml) / np.sqrt(
np.linalg.det(self.cov_samples))
resultdict['conservative_evidence'] = self.conservative_evidence
# Evidence from thermodynamic integration from the PT sampler
#############################################################
if self.config['SAMPLER'].lower() == 'paralleltempering':
self.logz, self.dlogz = self.sampler.log_evidence_estimate(
fburnin=0.)
resultdict['log_thd_evidence'] = self.logz
resultdict['dlog_thd_evidence'] = self.dlogz
# Posterior mean
# The posterior mean values of the parameters
###############
post_mean_vals = np.mean(self.sampler.flatchain, axis=0)
resultdict['post_mean_vals'] = post_mean_vals
# Likelihood
# The value of the posterior for the best-fit results
############
logL = self.sampler.log_prob_fn(post_mean_vals)
resultdict['logL'] = logL
# Save as .npz
np.savez(os.path.join(self.config['PROJECT_NAME'], 'output.npz'),
**resultdict)
def mcmc_mpi(Nwalkers, Niters, Mr, prior_name = 'first_try', pois = False):
'''
Parameters
-----------
- Nwalker :
Number of walkers
- Nchains :
Number of MCMC chains
'''
#data and covariance matrix
fake_obs_icov = Data.load_covariance(Mr , pois = False)
fake_obs = Data.load_data(Mr)
# True HOD parameters
data_hod = Data.load_dechod_random_guess(Mr)
Ndim = len(data_hod)
# Priors
prior_min, prior_max = PriorRange(prior_name , Mr)
prior_range = np.zeros((len(prior_min),2))
prior_range[:,0] = prior_min
prior_range[:,1] = prior_max
# mcmc chain output file
chain_file_name = ''.join([util.mcmc_dir(),'group_nopoisson_mcmc_chain_Mr',str(Mr),'.hdf5'])
if os.path.isfile(chain_file_name) and continue_chain:
print 'Continuing previous MCMC chain!'
sample = h5py.File(chain_file_name , "r")
Nchains = Niters - len(sample) # Number of chains left to finish
if Nchains > 0:
pass
else:
raise ValueError
print Nchains, ' iterations left to finish'
# Initializing Walkers from the end of the chain
pos0 = sample[-Nwalkers:]
else:
# new chain
print "chain_file_name=" , chain_file_name
sample_file = h5py.File(chain_file_name , 'w')
sample_file.create_dataset("mcmc",(Niters, Nwalkers, Ndim), data = np.zeros((Niters, Nwalkers , Ndim)))
sample_file.close()
# Initializing Walkers
random_guess = data_hod
pos0 = np.repeat(random_guess, Nwalkers).reshape(Ndim, Nwalkers).T + \
5.e-2 * np.random.randn(Ndim * Nwalkers).reshape(Nwalkers, Ndim)
print "initial position of the walkers = " , pos0.shape
# Initializing MPIPool
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
# Initializing the emcee sampler
hod_kwargs = {
'prior_range': prior_range,
'data': fake_obs,
'data_icov': fake_obs_icov,
'Mr': Mr
}
sampler = emcee.EnsembleSampler(Nwalkers, Ndim, lnPost, pool=pool, kwargs=hod_kwargs)
cnt = 0
# Initializing Walkers
for result in sampler.sample(pos0, iterations = Niters, storechain=False):
position = result[0]
sample_file = h5py.File(chain_file_name)
sample_file["mcmc"][cnt] = position
sample_file.close()
print "iteration=" , cnt
cnt += 1
pass
pool.close()
def run_emcee(run_name, nsteps, nwalkers, lnprob, to_vary):
"""The heart of it.
Args:
run_name (str): the name to output I guess
nsteps (int):
nwalkers (int):
lnprob (something):
to_vary (list of lists): list of [param name,
initial_position_center,
initial_position_sigma,
(prior low bound, prior high bound)]
for each parameter.
The second two values set the position & size
for a random Gaussian ball of initial positions
"""
# Something to do with parallelizing
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
# initiate sampler chain
ndim = len(to_vary)
sampler = emcee.EnsembleSampler(nwalkers,
ndim,
lnprob,
args=(run_name, to_vary),
pool=pool)
# Name the chain we're looking for
chain_filename = run_name + '/' + run_name + '_chain.csv'
# Try to resume an existing run of this name.
try:
# Read in an existing chain
chain = pd.read_csv(chain_filename)
start_step = chain.index[-1] // nwalkers
print 'Resuming {} at step {}'.format(run_name, start_step)
pos = np.array(chain.iloc[-nwalkers:, :-1])
# If we're adding new steps, just put in a new line and get started.
with open(chain_filename, 'a') as f:
f.write('\n')
end = np.array(chain.iloc[-nwalkers:, :])
print 'Start step: {}'.format(np.mean(end[:, -1]))
# If there's no pre-existing run, set one up.
except IOError:
sp.call(['mkdir', run_name])
sp.call(['mkdir', run_name + '/model_files'])
print 'Starting {}'.format(run_name)
start_step = 0
# Start a new file for the chain
# Set up a header line
with open(chain_filename, 'w') as f:
param_names = [param[0] for param in to_vary]
np.savetxt(f, (np.append(param_names, 'lnprob'), ),
delimiter=',',
fmt='%s')
# Set up initial positions?
"""I think this is saying the same thing as the nested list comps.
pos = []
for i in range(nwalkers):
for param in to_vary:
pos.append(param[1] + param[2]*np.random.randn())
"""
# randn makes an n-dimensional array of rands in [0,1]
pos = [[param[1] + param[2] * np.random.randn() for param in to_vary]
for i in range(nwalkers)]
# Initialize the lnprob list
lnprobs = []
first_sample = sampler.sample(pos, iterations=nsteps, storechain=False)
for i, result in enumerate(first_sample):
"""Enumerate returns a tuple the element and a counter.
tuples = [t for t in enumerate(['a', 'b', 'c'])]
counters = [c for c, l in enumerate(['a', 'b', 'c'])]
"""
old_lnprobs = np.copy(lnprobs)
pos, lnprobs, blob = result
print "Step {}: {}".format(start_step + i, np.mean(lnprobs))
# print('Acceptances: {}'.format([lnprob for lnprob in lnprobs if lnprob not in old_lnprobs]))
# print('')
# print(lnprobs)
# print(np.mean(pos))
# Log out the new positions
with open(chain_filename, 'a') as f:
new_step = [np.append(pos[k], lnprobs[k]) for k in range(nwalkers)]
np.savetxt(f, new_step, delimiter=',')
pool.close()
def run_emcee_simple(run_name,
nsteps,
nwalkers,
lnprob,
to_vary,
burn_in=0,
pool=False,
resume=False):
"""A new version of run_emcee.
Args:
run_name (str):
nsteps (int):
nwalkers (int):
lnprob (function?): I think lnprob here is a function?
Maybe equivalent in docs to lnpostfn
to_vary (list of lists):
burn_in (int?): how many steps to remove from the front
pool (bool): Want to parallelize?
resume (bool): Are you resuming a previous run?
"""
# Set up parallelization
if pool:
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
start = time.time()
# initiate sampler chain
ndim = len(to_vary[0])
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, pool=pool)
# Name the chain we're looking for
chain_filename = run_name + '/' + run_name + '_chain.csv'
# This seems a little risky bc if you forget, you just overwrite.
if resume:
chain = pd.read_csv(chain_filename)
start_step = chain.index[-1] // nwalkers
print('Resuming {} at step {}'.format(run_name, start_step))
with open(chain_filename, 'a') as f:
f.write('\n')
pos = np.array(chain.iloc[-nwalkers:, :-1])
else:
sp.call('rm -rf ' + run_name, shell=True)
sp.call(['mkdir', run_name])
print('Starting {}'.format(run_name))
start_step = 0
with open(chain_filename, 'w') as f:
f.write(','.join([param[0]
for param in to_vary] + ['lnprob']) + '\n')
pos = [[param[1] + param[2] * np.random.randn() for param in to_vary]
for i in range(nwalkers)]
# Run the sampler and then query it
run = sampler.sample(pos, iterations=nsteps, storechain=False)
"""Note that sampler.sample returns:
pos: list of the walkers' current positions in an object of shape
[nwalkers, ndim]
lnprob: The list of log posterior probabilities for the walkers at
positions given by pos.
The shape of this object is (nwalkers, dim)
rstate: The current state of the random number generator.
blobs (optional): The metadata "blobs" associated with the current
position. The value is only returned if
lnpostfn returns blobs too.
"""
for i, result in enumerate(run):
print "Step {}".format(start_step + i)
# Where did chisum come from? What is it returning?
pos, chisum, blob = result
with open(run_name + '/' + run_name + '_chain.csv', 'a') as f:
for i in range(nwalkers):
f.write(','.join(map(str, np.append(pos[i], chisum[i]))) +
'\n')
print('{} samples in {:.1f} seconds'.format(nsteps * nwalkers,
time.time() - start))
if pool:
pool.close()
return MCMCrun(run_name, nwalkers, burn_in=burn_in)
def LensModelMCMC(data,lens,source,
xmax=30.,highresbox=[-3.,3.,-3.,3.],emitres=None,fieldres=None,
sourcedatamap=None, scaleamp=False, shiftphase=False,
modelcal=True,cosmo=Planck15,
nwalkers=1e3,nburn=1e3,nstep=1e3,pool=None,nthreads=1,mpirun=False):
"""
Wrapper function which basically takes what the user wants and turns it into the
format needed for the acutal MCMC lens modeling.
Inputs:
data:
One or more visdata objects; if multiple datasets are being
fit to, should be a list of visdata objects.
lens:
Any of the currently implemented lens objects or ExternalShear.
source:
One or more of the currently implemented source objects; if more than
one source to be fit, should be a list of multiple sources.
xmax:
(Half-)Grid size, in arcseconds; the grid will span +/-xmax in x&y
highresbox:
The region to model at higher resolution (to account for high-magnification
and differential lensing effects), as [xmin, xmax, ymin, ymax].
Note the sign convention is: +x = West, +y = North, like the lens
positions.
sourcedatamap:
A list of length the number of datasets which tells which source(s)
are to be fit to which dataset(s). Eg, if two sources are to be fit
to two datasets jointly, should be [[0,1],[0,1]]. If we have four
sources and three datasets, could be [[0,1],[0,1],[2,3]] to say that the
first two sources should both be fit to the first two datasets, while the
second two should be fit to the third dataset. If None, will assume
all sources should be fit to all datasets.
scaleamp:
A list of length the number of datasets which tells whether a flux
rescaling is allowed and which dataset the scaling should be relative to.
False indicates no scaling should be done, while True indicates that
amplitude scaling should be allowed.
shiftphase:
Similar to scaleamp above, but allowing for positional/astrometric offsets.
modelcal:
Whether or not to perform the pseudo-selfcal procedure of H+13
cosmo:
The cosmology to use, as an astropy object, e.g.,
from astropy.cosmology import WMAP9; cosmo=WMAP9
Default is Planck15.
nwalkers:
Number of walkers to use in the mcmc process; see dan.iel.fm/emcee/current
for more details.
nburn:
Number of burn-in steps to take with the chain.
nstep:
Number of actual steps to take in the mcmc chains after the burn-in
nthreads:
Number of threads (read: cores) to use during the fitting, default 1.
mpirun:
Whether to parallelize using MPI instead of multiprocessing. If True,
nthreads has no effect, and your script should be run with, eg,
mpirun -np 16 python lensmodel.py.
Returns:
mcmcresult:
A nested dict containing the chains requested. Will have all the MCMC
chain results, plus metadata about the run (initial params, data used,
etc.). Formatting still a work in progress (esp. for modelcal phases).
chains:
The raw chain data, for testing.
blobs:
Everything else returned by the likelihood function; will have
magnifications and any modelcal phase offsets at each step; eventually
will remove this once get everything packaged up for mcmcresult nicely.
colnames:
Basically all the keys to the mcmcresult dict; eventually won't need
to return this once mcmcresult is packaged up nicely.
"""
if pool: nthreads = 1
elif mpirun:
nthreads = 1
from emcee.utils import MPIPool
pool = MPIPool(debug=False,loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
else: pool = None
# Making these lists just makes later stuff easier since we now know the dtype
lens = list(np.array([lens]).flatten())
source = list(np.array([source]).flatten()) # Ensure source(s) are a list
data = list(np.array([data]).flatten()) # Same for dataset(s)
scaleamp = list(np.array([scaleamp]).flatten())
shiftphase = list(np.array([shiftphase]).flatten())
modelcal = list(np.array([modelcal]).flatten())
if len(scaleamp)==1 and len(scaleamp)<len(data): scaleamp *= len(data)
if len(shiftphase)==1 and len(shiftphase)<len(data): shiftphase *= len(data)
if len(modelcal)==1 and len(modelcal)<len(data): modelcal *= len(data)
if sourcedatamap is None: sourcedatamap = [None]*len(data)
# emcee isn't very flexible in terms of how it gets initialized; start by
# assembling the user-provided info into a form it likes
ndim, p0, colnames = 0, [], []
# Lens(es) first
for i,ilens in enumerate(lens):
if ilens.__class__.__name__=='SIELens':
for key in ['x','y','M','e','PA']:
if not vars(ilens)[key]['fixed']:
ndim += 1
p0.append(vars(ilens)[key]['value'])
colnames.append(key+'L'+str(i))
elif ilens.__class__.__name__=='ExternalShear':
for key in ['shear','shearangle']:
if not vars(ilens)[key]['fixed']:
ndim += 1
p0.append(vars(ilens)[key]['value'])
colnames.append(key)
# Then source(s)
for i,src in enumerate(source):
if src.__class__.__name__=='GaussSource':
for key in ['xoff','yoff','flux','width']:
if not vars(src)[key]['fixed']:
ndim += 1
p0.append(vars(src)[key]['value'])
colnames.append(key+'S'+str(i))
elif src.__class__.__name__=='SersicSource':
for key in ['xoff','yoff','flux','majax','index','axisratio','PA']:
if not vars(src)[key]['fixed']:
ndim += 1
p0.append(vars(src)[key]['value'])
colnames.append(key+'S'+str(i))
elif src.__class__.__name__=='PointSource':
for key in ['xoff','yoff','flux']:
if not vars(src)[key]['fixed']:
ndim += 1
p0.append(vars(src)[key]['value'])
colnames.append(key+'S'+str(i))
# Then flux rescaling; only matters if >1 dataset
for i,t in enumerate(scaleamp[1:]):
if t:
ndim += 1
p0.append(1.) # Assume 1.0 scale factor to start
colnames.append('ampscale_dset'+str(i+1))
# Then phase/astrometric shift; each has two vals for a shift in x&y
for i,t in enumerate(shiftphase[1:]):
if t:
ndim += 2
p0.append(0.); p0.append(0.) # Assume zero initial offset
colnames.append('astromshift_x_dset'+str(i+1))
colnames.append('astromshift_y_dset'+str(i+1))
# Get any model-cal parameters set up. The process involves some expensive
# matrix inversions, but these only need to be done once, so we'll do them
# now and pass the results as arguments to the likelihood function. See docs
# in calc_likelihood.model_cal for more info.
for i,dset in enumerate(data):
if modelcal[i]:
uniqant = np.unique(np.asarray([dset.ant1,dset.ant2]).flatten())
dPhi_dphi = np.zeros((uniqant.size-1,dset.u.size))
for j in range(1,uniqant.size):
dPhi_dphi[j-1,:]=(dset.ant1==uniqant[j])-1*(dset.ant2==uniqant[j])
C = scipy.sparse.diags((dset.sigma/dset.amp)**-2.,0)
F = np.dot(dPhi_dphi,C*dPhi_dphi.T)
Finv = np.linalg.inv(F)
FdPC = np.dot(-Finv,dPhi_dphi*C)
modelcal[i] = [dPhi_dphi,FdPC]
# Create our lensing grid coordinates now, since those shouldn't be
# recalculated with every call to the likelihood function
xmap,ymap,xemit,yemit,indices = GenerateLensingGrid(data,xmax,highresbox,
fieldres,emitres)
# Calculate the uv coordinates we'll interpolate onto; only need to calculate
# this once, so do it here.
kmax = 0.5/((xmap[0,1]-xmap[0,0])*arcsec2rad)
ug = np.linspace(-kmax,kmax,xmap.shape[0])
# Calculate some distances; we only need to calculate these once.
# This assumes multiple sources are all at same z; should be this
# way anyway or else we'd have to deal with multiple lensing planes
if cosmo is None: cosmo = Planck15
Dd = cosmo.angular_diameter_distance(lens[0].z).value
Ds = cosmo.angular_diameter_distance(source[0].z).value
Dds= cosmo.angular_diameter_distance_z1z2(lens[0].z,source[0].z).value
p0 = np.array(p0)
# Create a ball of starting points for the walkers, gaussian ball of
# 10% width; if initial value is 0 (eg, astrometric shift), give a small sigma
# for angles, generally need more spread than 10% to sample well, do 30% for those cases [~0.5% >180deg for p0=100deg]
isangle = np.array([0.30 if 'PA' in s or 'angle' in s else 0.1 for s in colnames])
initials = emcee.utils.sample_ball(p0,np.asarray([isangle[i]*x if x else 0.05 for i,x in enumerate(p0)]),int(nwalkers))
# All the lens objects know if their parameters have been altered since the last time
# we calculated the deflections. If all the lens pars are fixed, we only need to do the
# deflections once. This step ensures that the lens object we create the sampler with
# has these initial deflections.
for i,ilens in enumerate(lens):
if ilens.__class__.__name__ == 'SIELens': ilens.deflect(xemit,yemit,Dd,Ds,Dds)
elif ilens.__class__.__name__ == 'ExternalShear': ilens.deflect(xemit,yemit,lens[0])
# Create the sampler object; uses calc_likelihood function defined elsewhere
lenssampler = emcee.EnsembleSampler(nwalkers,ndim,calc_vis_lnlike,
args = [data,lens,source,Dd,Ds,Dds,ug,
xmap,ymap,xemit,yemit,indices,
sourcedatamap,scaleamp,shiftphase,modelcal],
threads=nthreads,pool=pool)
# Run burn-in phase
print "Running burn-in... "
#pos,prob,rstate,mus = lenssampler.run_mcmc(initials,nburn,storechain=False)
for i,result in enumerate(lenssampler.sample(initials,iterations=nburn,storechain=False)):
if i%20==0: print 'Burn-in step ',i,'/',nburn
pos,prob,rstate,blob = result
lenssampler.reset()
# Run actual chains
print "Done. Running chains... "
for i,result in enumerate(lenssampler.sample(pos,rstate0=rstate,iterations=nstep,storechain=True)):
if i%20==0: print 'Chain step ',i,'/',nstep
#lenssampler.run_mcmc(pos,nstep,rstate0=rstate)
if mpirun: pool.close()
print "Mean acceptance fraction: ",np.mean(lenssampler.acceptance_fraction)
#return lenssampler.flatchain,lenssampler.blobs,colnames
# Package up the magnifications and modelcal phases; disregards nan points (where
# we failed the prior, usu. because a periodic angle wrapped).
blobs = lenssampler.blobs
mus = np.asarray([[a[0] for a in l] for l in blobs]).flatten(order='F')
bad = np.where(np.asarray([np.any(np.isnan(m)) for m in mus],dtype=bool))[0]
for k in bad: mus[k] = np.array([np.nan]*len(source))
mus = np.asarray(list(mus),dtype=float).reshape((-1,len(source)),order='F') # stupid-ass hack
bad = np.isnan(mus)[:,0]
#bad = bad.reshape((-1,len(source)),order='F')[:,0]
#mus = np.atleast_2d(np.asarray([mus[i] if not bad[i] else [np.nan]*len(source) for i in range(mus.size)])).T
colnames.extend(['mu{0:.0f}'.format(i) for i in range(len(source))])
# Assemble the output. Want to return something that contains both the MCMC chains
# themselves, but also metadata about the run.
mcmcresult = {}
# keep track of git revision, for reproducibility's sake
# if run under mpi, this will spew some scaremongering warning text,
# but it's fine. use --mca mpi_warn_on_fork 0 in the mpirun statement to disable
try:
import subprocess
gitd = os.path.abspath(os.path.join(os.path.dirname(__file__),os.pardir))
mcmcresult['githash'] = subprocess.check_output('git --git-dir={0:s} --work-tree={1:s} '\
'rev-parse HEAD'.format(gitd+'/.git',gitd),shell=True).rstrip()
except:
mcmcresult['githash'] = 'No repo found'
mcmcresult['datasets'] = [dset.filename for dset in data] # Data files used
mcmcresult['lens_p0'] = lens # Initial params for lens,src(s),shear; also tells if fixed, priors, etc.
mcmcresult['source_p0'] = source
if sourcedatamap: mcmcresult['sourcedatamap'] = sourcedatamap
mcmcresult['xmax'] = xmax
mcmcresult['highresbox'] = highresbox
mcmcresult['fieldres'] = fieldres
mcmcresult['emitres'] = emitres
if any(scaleamp): mcmcresult['scaleamp'] = scaleamp
if any(shiftphase): mcmcresult['shiftphase'] = shiftphase
mcmcresult['chains'] = np.core.records.fromarrays(np.hstack((lenssampler.flatchain[~bad],mus[~bad])).T,names=colnames)
mcmcresult['lnlike'] = lenssampler.flatlnprobability[~bad]
# Keep track of best-fit params, derived from chains.
c = copy.deepcopy(mcmcresult['chains'])
mcmcresult['best-fit'] = {}
pbest = []
# Calculate the best fit values as medians of each param
lens,source = copy.deepcopy(mcmcresult['lens_p0']), copy.deepcopy(mcmcresult['source_p0'])
for i,ilens in enumerate(lens):
if ilens.__class__.__name__ == 'SIELens':
ilens.__dict__['_altered'] = True
for key in ['x','y','M','e','PA']:
if not vars(ilens)[key]['fixed']:
ilens.__dict__[key]['value'] = np.median(c[key+'L'+str(i)])
pbest.append(np.median(c[key+'L'+str(i)]))
elif ilens.__class__.__name__ == 'ExternalShear':
for key in ['shear','shearangle']:
if not vars(ilens)[key]['fixed']:
ilens.__dict__[key]['value'] = np.median(c[key])
pbest.append(np.median(c[key]))
mcmcresult['best-fit']['lens'] = lens
# now do the source(s)
for i,src in enumerate(source): # Source is a list of source objects
if src.__class__.__name__ == 'GaussSource':
for key in ['xoff','yoff','flux','width']:
if not vars(src)[key]['fixed']:
src.__dict__[key]['value'] = np.median(c[key+'S'+str(i)])
pbest.append(np.median(c[key+'S'+str(i)]))
elif src.__class__.__name__ == 'SersicSource':
for key in ['xoff','yoff','flux','majax','index','axisratio','PA']:
if not vars(src)[key]['fixed']:
src.__dict__[key]['value'] = np.median(c[key+'S'+str(i)])
pbest.append(np.median(c[key+'S'+str(i)]))
elif src.__class__.__name__ == 'PointSource':
for key in ['xoff','yoff','flux']:
if not vars(src)[key]['fixed']:
src.__dict__[key]['value'] = np.median(c[key+'S'+str(i)])
pbest.append(np.median(c[key+'S'+str(i)]))
mcmcresult['best-fit']['source'] = source
mcmcresult['best-fit']['magnification'] = np.median(mus[~bad],axis=0)
# Any amplitude scaling or astrometric shifts
bfscaleamp = np.ones(len(data))
if 'scaleamp' in mcmcresult.keys():
for i,t in enumerate(mcmcresult['scaleamp']): # only matters if >1 datasets
if i==0: pass
elif t:
bfscaleamp[i] = np.median(c['ampscale_dset'+str(i)])
pbest.append(np.median(c['ampscale_dset'+str(i)]))
else: pass
mcmcresult['best-fit']['scaleamp'] = bfscaleamp
bfshiftphase = np.zeros((len(data),2))
if 'shiftphase' in mcmcresult.keys():
for i,t in enumerate(mcmcresult['shiftphase']):
if i==0: pass # only matters if >1 datasets
elif t:
bfshiftphase[i][0] = np.median(c['astromshift_x_dset'+str(i)])
bfshiftphase[i][1] = np.median(c['astromshift_y_dset'+str(i)])
pbest.append(np.median(c['astromshift_x_dset'+str(i)]))
pbest.append(np.median(c['astromshift_y_dset'+str(i)]))
else: pass # no shifting
mcmcresult['best-fit']['shiftphase'] = bfshiftphase
mcmcresult['best-fit']['lnlike'] = calc_vis_lnlike(pbest,data,mcmcresult['best-fit']['lens'],
mcmcresult['best-fit']['source'],
Dd,Ds,Dds,ug,xmap,ymap,xemit,yemit,indices,
sourcedatamap,scaleamp,shiftphase,modelcal)[0]
# Calculate the deviance information criterion, using the Spiegelhalter+02 definition (cf Gelman+04)
mcmcresult['best-fit']['DIC'] = -4*np.mean(mcmcresult['lnlike']) + 2*mcmcresult['best-fit']['lnlike']
# If we did any modelcal stuff, keep the antenna phase offsets here
if any(modelcal):
mcmcresult['modelcal'] = [True if j else False for j in modelcal]
dp = np.squeeze(np.asarray([[a[1] for a in l if ~np.any(np.isnan(a[0]))] for l in blobs]))
a = [x for l in dp for x in l] # Have to dick around with this if we had any nan's
dphases = np.squeeze(np.reshape(a,(nwalkers*nstep-bad.sum(),len(data),-1),order='F'))
if len(data) > 1:
for i in range(len(data)):
if modelcal[i]: mcmcresult['calphases_dset'+str(i)] = np.vstack(dphases[:,i])
else:
if any(modelcal): mcmcresult['calphases_dset0'] = dphases
return mcmcresult
def mcmc_mpi(
Nwalkers,
Nchains,
observables=["nbar", "xi"],
data_dict={"Mr": 21, "b_normal": 0.25},
prior_name="first_try",
mcmcrun=None,
):
"""
Standard MCMC implementaion
Parameters
-----------
- Nwalker :
Number of walkers
- Nchains :
Number of MCMC chains
- observables :
list of observables. Options are: ['nbar','xi'],['nbar','gmf'],['xi']
- data_dict : dictionary that specifies the observation keywords
"""
# Initializing the vector of observables and inverse covariance matrix
if observables == ["xi"]:
fake_obs = Data.data_xi(**data_dict)
# fake_obs_icov = Data.data_inv_cov('xi', **data_dict)
fake_obs_icov = Data.data_cov(inference="mcmc", **data_dict)[1:16, 1:16]
if observables == ["nbar", "xi"]:
fake_obs = np.hstack([Data.data_nbar(**data_dict), Data.data_xi(**data_dict)])
fake_obs_icov = Data.data_cov(inference="mcmc", **data_dict)[:16, :16]
if observables == ["nbar", "gmf"]:
##### FIRST BIN OF GMF DROPPED ###############
# CAUTION: hardcoded
fake_obs = np.hstack([Data.data_nbar(**data_dict), Data.data_gmf(**data_dict)[1:]])
fake_obs_icov = np.zeros((10, 10))
# print Data.data_cov(**data_dict)[17: , 17:].shape
# Covariance matrix being adjusted accordingly
fake_obs_icov[1:, 1:] = Data.data_cov(inference="mcmc", **data_dict)[17:, 17:]
fake_obs_icov[0, 1:] = Data.data_cov(inference="mcmc", **data_dict)[0, 17:]
fake_obs_icov[1:, 0] = Data.data_cov(inference="mcmc", **data_dict)[17:, 0]
fake_obs_icov[0, 0] = Data.data_cov(inference="mcmc", **data_dict)[0, 0]
# True HOD parameters
data_hod_dict = Data.data_hod_param(Mr=data_dict["Mr"])
data_hod = np.array(
[
data_hod_dict["logM0"], # log M0
np.log(data_hod_dict["sigma_logM"]), # log(sigma)
data_hod_dict["logMmin"], # log Mmin
data_hod_dict["alpha"], # alpha
data_hod_dict["logM1"], # log M1
]
)
Ndim = len(data_hod)
# Priors
prior_min, prior_max = PriorRange(prior_name)
prior_range = np.zeros((len(prior_min), 2))
prior_range[:, 0] = prior_min
prior_range[:, 1] = prior_max
# mcmc chain output file
chain_file = "".join([util.mcmc_dir(), util.observable_id_flag(observables), ".", mcmcrun, ".mcmc_chain.dat"])
# print chain_file
if os.path.isfile(chain_file) and continue_chain:
print "Continuing previous MCMC chain!"
sample = np.loadtxt(chain_file)
Nchain = Niter - (len(sample) / Nwalkers) # Number of chains left to finish
if Nchain > 0:
pass
else:
raise ValueError
print Nchain, " iterations left to finish"
# Initializing Walkers from the end of the chain
pos0 = sample[-Nwalkers:]
else:
# new chain
f = open(chain_file, "w")
f.close()
Nchain = Niter
# Initializing Walkers
random_guess = data_hod
pos0 = np.repeat(random_guess, Nwalkers).reshape(Ndim, Nwalkers).T + 5.0e-2 * np.random.randn(
Ndim * Nwalkers
).reshape(Nwalkers, Ndim)
# print pos0.shape
# Initializing MPIPool
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
# Initializing the emcee sampler
hod_kwargs = {
"prior_range": prior_range,
"data": fake_obs,
"data_icov": fake_obs_icov,
"observables": observables,
"Mr": data_dict["Mr"],
}
sampler = emcee.EnsembleSampler(Nwalkers, Ndim, lnPost, pool=pool, kwargs=hod_kwargs)
# Initializing Walkers
for result in sampler.sample(pos0, iterations=Nchain, storechain=False):
position = result[0]
# print position
f = open(chain_file, "a")
for k in range(position.shape[0]):
output_str = "\t".join(position[k].astype("str")) + "\n"
f.write(output_str)
f.close()
pool.close()
def run(N):
fn = chainDirRel + '.pickle'
nwalkers = 500
ndim = 9 # 15
#eta, epsff, fg0, muNorm, muScaling, fixedQ, accScaleLength, xiREC, accNorm, accAlphaZ, accAlphaMh, accCeiling, fcool, kappaMetals, ZIGM = emceeParams
#p00 = np.array([ .9, .1, -1., .08, .50959, .38, -.25, .7, .01 ])
#p0 = [p00*(1.0+0.2*np.random.randn( ndim )) for i in range(nwalkers)]
p0 = [sampleFromPrior() for i in range(nwalkers)]
restart = {}
restart['currentPosition'] = p0
restart['chain'] = None
restart['state'] = None
restart['prob'] = None
restart['iterationCounter'] = 0
restart['mcmcRunCounter'] = 0
updateRestart(fn, restart)
global runNumber
runNumber = restart['mcmcRunCounter']
restart['iterationCounter'] += N
restart['mcmcRunCounter'] += 1
pool = MPIPool(comm=comm, loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnProb, pool=pool)
#pos, prob, state = sampler.run_mcmc(restart['currentPosition'], N, rstate0=restart['state'], lnprob0=restart['prob'])
counter = 0
for result in sampler.sample(restart['currentPosition'],
iterations=N,
lnprob0=restart['prob'],
rstate0=restart['state']):
print "Beginning iteration number ", counter, " of ", N
pos, prob, state = result
restart[
'acor'] = sampler.acor[:] # autocorr length for each param (ndim)
restart[
'accept'] = sampler.acceptance_fraction[:] # acceptance frac for each walker.
restart['currentPosition'] = pos # same shape as p0: nwalkers x ndim
restart['state'] = state # random number generator state
restart['prob'] = prob # nwalkers x dim
if restart['chain'] is None:
restart['chain'] = sampler.chain # nwalkers x niterations x ndim
else:
print np.shape(restart['chain']), np.shape(
sampler.chain[:, -1, :]), np.shape(sampler.chain)
print restart['mcmcRunCounter'], restart['iterationCounter']
#restart['chain'] = np.concatenate((restart['chain'], sampler.chain[:,-1,:]), axis=1)
print "dbg1: ", np.shape(restart['chain']), np.shape(
np.zeros(
(nwalkers, 1, ndim))), np.shape(np.expand_dims(pos, 1))
restart['chain'] = np.concatenate(
(restart['chain'], np.expand_dims(pos, 1)), axis=1)
saveRestart(fn, restart)
counter += 1
pool.close()
def emceeinit(w0, inclin, nbins, nthreads, nsteps, savename, data, dbins, MPI=0, allbinseq=0):
"""Emcee driver function"""
#HARDCODED - Warning. Also bins.
global incl
incl = inclin
#Initialize the MPI-based pool used for parallelization.
if MPI:
print MPI
pool = MPIPool()
if not pool.is_master():
# Wait for instructions from the master process.
pool.wait()
sys.exit(0)
#Setup
ndim = nbins #Removing inclination as a variable.
nwalkers = 4*ndim
p0 = np.zeros((nwalkers, ndim))
print 'Nbins is now', nbins
#Needed for fixing unresolved starting balls
global b1
global rin
rin, b1 = dbins
#Initialize walkers
radii = np.arange(nbins)
sizecorr = 1 #Currently Hardcoded; Scaling factor to treat different radii differently
scale = 0.2 #Currently hardcoded; Fraction of parameter by which it can vary
for walker in range(nwalkers):
for rs in radii:
rand = np.random.uniform(-(w0[rs]*scale*sizecorr), (w0[rs]*scale*sizecorr))
if (b1[rs] <= res) and (allbinseq <1) :
rand = np.random.uniform(0, 2.*w0[rs])
p0[walker][rs] = w0[rs] + rand #Make it rs+2, if a & l vary
# #Initialize a & l
# p0[walker][0] = np.random.uniform(.0001, .5) #When adding back in, make prev statement rs+1
# while True:
# p0[walker][1] = np.random.gamma(2., 2.)*np.amax(dbins[1:])/20. + np.amin(np.diff(dbins[1:]))
# if (p0[walker][1]>=np.amin(dbins[1:]) or p0[walker][1]<=np.amax(dbins[1:])):
# break
#THIS IS A PROBLEM FOR THE 1st BIN WITH rin. Also the normalization
# p0[walker][0] = incl+np.random.uniform(0.85*incl,1.15*incl) #When adding back in, make prev statement rs+1
#Write emcee perturbation params to log file
f = open('emceerand.log', 'a')
FORMAT = '%m-%d-%Y-%H%M'
f.write(savename+', '+str(nbins)+', '+str(nsteps)+', '+str(scale)+', '+str(sizecorr)+', '+datetime.now().strftime(FORMAT))
#Model initialization
u, v, dreal, dimag, dwgt = data
udeproj = u * np.cos(incl) #Deproject
rho = 1e3*np.sqrt(udeproj**2+v**2)
indices = np.arange(b1.size)
global gpbins
gpbins = dbins
#rin, indices
global rbin
rbin = np.concatenate([np.array([rin]), b1])
jarg = np.outer(2.*np.pi*rbin, rho/206264.806427)
global jinc
jinc = sc.j1(jarg)/jarg
# pool = mp.Pool(nthreads-1)
#Initialize sampler using MPI if necessary
if MPI:
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, pool=pool)
else:
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, threads=nthreads)
print 'Nbins, Ndim', nbins, ndim
print 'Dbins', dbins
#Run emcee, and time it
tic = time.time()
print "I'm line 110, before the threads"
sampler.run_mcmc(p0, nsteps)
print "I'm line 112, after the threads"
toc = time.time()
#Display and record run information
print 'Elapsed emcee run time:', ((toc-tic)/60.)
print 'Acceptance:', sampler.acceptance_fraction
f.write(' ,'+str(round((toc-tic)/60., 2))+', '+str(np.round(np.mean(sampler.acceptance_fraction),2))+'\n')
f.close()
#Save the results in a binary file
np.save('mc_'+savename,sampler.chain)
if MPI:
#Close the processes.
pool.close()
print 'Done with this emcee run'
#Allow user interaction at end, if not using MPI
# if not MPI:
# pdb.set_trace()
return sampler.chain
def fit_BAO():
parser = argparse.ArgumentParser(description='Use mcmc routine to get the BAO peak stretching parameter alpha and damping parameter, made by Zhejie.',\
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
"--lt",
help=
'*The type of weak lensing survey. (TF: Tully-Fisher; TW: traditional (photo-z) weak lensing.)',
required=True)
parser.add_argument("--nrbin",
help='*Number of tomographic bins.',
type=int,
required=True)
parser.add_argument("--nkbin",
help='*Number of output k bins.',
type=int,
required=True)
parser.add_argument("--shapenf",
help='*Shape noise factor.',
required=True)
parser.add_argument("--kmin", help='*kmin fit boundary.', required=True)
parser.add_argument("--kmax", help='*kmax fit boundary.', required=True)
parser.add_argument("--params_str",
help='Set fitting parameters. 1: free; 0: fixed.',
required=True)
parser.add_argument("--Sigma2_inf",
help='Whether setting Sigma2_xy as infinity or not.',
default='False')
parser.add_argument("--alpha",
help='Fix the parameter alpha value.',
default=1.0,
type=np.float)
parser.add_argument(
"--Pwig_type",
help=
'*The spatial P(k)_wig whether is linear or not. Type Pwig_linear or Pwig_nonlinear; in nonlinear, BAO is damped.',
required=True)
parser.add_argument(
"--Psm_type",
help=
'The expression of Pnorm. The default case, Pnorm from Eisenstein & Zaldarriaga 1999. \
Test Pnorm=Pnow, which is derived from transfer function.'
)
#parser.add_argument("--Sigma", help = 'BAO damping parameter Sigma value. (Either 0.0 or 100.0.)', type=float, required=True)
parser.add_argument(
"--survey_stage",
help=
'Optional parameter. KW_stage_IV (kinematic weak lensing) or PW_stage_IV (photo-z). It could also be considered as the directory of data\
files to be fitted.')
#parser.add_argument("--mpi_used", help = 'Whether MPI is implemented in the calculation of Cijl_prime, Gm_prime. Either True or False.')
parser.add_argument(
"--f_sky",
help=
'This addtional argument is for data files in TF_cross-ps. Distinguish cases with different f_sky value.'
)
parser.add_argument(
"--set_SVc_on_CovP",
help=
'*Whether we replace smaller SV to be SVc in W matrix for the output inverse covariance matrix of Pk. Either True or False.',
required=True)
parser.add_argument(
"--start_lmin",
help=
"*The minimum ell value considered in the analysis. Default is 1. For Stage III, it's 10 for Stage III and 4 for Stage IV",
default=1,
type=int)
parser.add_argument(
"--nSV_min",
help=
"Fitting the extracted power spectrum with nSV used. nSV_min is the strating point.",
type=int,
default=1)
parser.add_argument(
"--save_sampler",
help=
"Whether we save samplers of MCMC into a data file or not. True or False.",
default='False')
parser.add_argument(
"--modify_Cov_cij_cpq",
help=
"Whether we have modified the Cov_cij_cpq while outputing Cijl^prime and Gm^prime.",
default='False')
args = parser.parse_args()
#print("args: ", args.lt)
lt = args.lt
num_rbin = args.nrbin
num_kbin = args.nkbin
shapenf = args.shapenf
kmin = float(args.kmin)
kmax = float(args.kmax)
params_str = args.params_str
params_indices = [int(i) for i in params_str]
Pwig_type = args.Pwig_type
Psm_type = args.Psm_type
survey_stage = args.survey_stage
#mpi_used = args.mpi_used
f_sky = args.f_sky
set_SVc_on_CovP = args.set_SVc_on_CovP
start_lmin = args.start_lmin
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
lt_prefix = {'TF': 'TF', 'TW': 'TW_zext'}
old_stdout = sys.stdout
if survey_stage:
odir = './{}/fit_kmin{}_kmax{}_Pwig_over_Pnow/{}/'.format(
survey_stage, kmin, kmax, Pwig_type)
else:
odir = './fit_kmin{}_kmax{}_Pwig_over_Pnow_fsky{}/{}/'.format(
kmin, kmax, f_sky, Pwig_type)
# if mpi_used == 'True':
# odir = './{}/fit_kmin{}_kmax{}_Pwig_over_Pnow/mpi_{}/'.format(survey_stage, kmin, kmax, Pwig_type)
if Psm_type == 'Pnow':
odir = odir + 'set_Pnorm_Pnow/'
if start_lmin != 1:
odir = odir + 'start_ell_{}/'.format(start_lmin)
if rank == 0:
if not os.path.exists(odir):
os.makedirs(odir)
comm.Barrier()
Sigma2_xy_dict = {'stage_III': 31.176, 'stage_IV': 22.578}
for ss_name in Sigma2_xy_dict:
if ss_name in survey_stage:
stage_name = ss_name
if Pwig_type == 'Pwig_nonlinear':
Sigma2_xy = Sigma2_xy_dict[stage_name]
elif Pwig_type == 'Pwig_linear':
Sigma2_xy = 0.0
if args.Sigma2_inf == 'True':
#Sigma2_xy = np.inf
Sigma2_xy = 100 * 100 # test whether it influences results or not
ofile = odir + "mcmc_fit_{}_{}rbin_{}kbin_snf{}_params{}_Sigma2_{}.log".format(
lt, num_rbin, num_kbin, shapenf, params_str, Sigma2_xy)
if params_str == '001':
ofile = odir + "mcmc_fit_{0}_{1}rbin_{2}kbin_snf{3}_params{4}_alpha{5:.2f}_Sigma2_{6}.log".format(
lt, num_rbin, num_kbin, shapenf, params_str, args.alpha, Sigma2_xy)
log_file = open(ofile, "w")
sys.stdout = log_file
print('Arguments of fitting: ', args)
ifile = '../Input_files/CAMB_Planck2015_matterpower.dat'
kcamb, Pkcamb = np.loadtxt(ifile, dtype='f8', comments='#', unpack=True)
Pwig_spl = InterpolatedUnivariateSpline(kcamb, Pkcamb)
k_0 = 0.001 # unit h*Mpc^-1
Pk_0 = Pwig_spl(k_0)
ifile = '../Input_files/transfer_fun_Planck2015.dat'
kk, Tf = np.loadtxt(ifile,
dtype='f8',
comments='#',
usecols=(0, 1),
unpack=True)
#print kk==kcamb
Tf_spl = InterpolatedUnivariateSpline(kk, Tf)
Tf_0 = Tf_spl(k_0)
P0_a = Pk_0 / (pow(k_0, cosmic_params.ns) * Tf_0**2.0)
Psm = P0_a * pow(
kcamb, cosmic_params.ns
) * Tf**2.0 # Get primordial (smooth) power spectrum from the transfer function
Psm_spl = InterpolatedUnivariateSpline(kcamb, Psm)
norm_gf = 1.0
N_walkers = 40
all_param_names = 'alpha', 'Sigma2_xy', 'A'
all_temperature = 0.01, 1.0, 0.1
alpha, A = args.alpha, 1.0 # initial guess for fitting, the value of Sigma2_xy at z=0.65 is from theory prediction (see code TF_cross_convergence_ps_bin.py)
all_params = alpha, Sigma2_xy, A
N_params, theta, fix_params, params_T, params_name = set_params(
all_params, params_indices, all_param_names, all_temperature)
# Fit for DM power spectrum
if lt == 'TF':
idir0 = '../{}_cross-ps/'.format(lt)
if survey_stage:
idir0 = '../{}/'.format(survey_stage)
idir1 = '{}_Pk_output_dset_{}/'
# if mpi_used == 'True':
# idir1 = 'mpi_{}_Pk_output_dset_{}/'
if f_sky:
idir1 = '{}_Pk_output_dset_{}_fsky{}/'
elif lt == 'TW':
idir0 = '../{}_f2py_SVD/'.format(lt)
if survey_stage:
idir0 = '../{}/'.format(survey_stage)
idir1 = '{}_Pk_output_dset_{}/'
idir2 = '{}rbins_{}kbins_snf{}/'.format(num_rbin, num_kbin, shapenf)
odir1 = 'mcmc_fit_params_Pwig_over_Pnow/{}/kmin{}_kmax{}/{}rbins_{}kbins_snf{}/'.format(
Pwig_type, kmin, kmax, num_rbin, num_kbin, shapenf)
if f_sky:
odir1 = 'mcmc_fit_params_Pwig_over_Pnow/{}/kmin{}_kmax{}/{}rbins_{}kbins_snf{}_fsky{}/'.format(
Pwig_type, kmin, kmax, num_rbin, num_kbin, shapenf, f_sky)
# if mpi_used == 'True':
# odir1 = 'mcmc_fit_params_Pwig_over_Pnow/{}/kmin{}_kmax{}/mpi_{}rbins_{}kbins_snf{}/'.format(Pwig_type, kmin, kmax, num_rbin, num_kbin, shapenf)
if Psm_type == 'Pnow':
idir2 = idir2 + 'set_Pnorm_Pnow/'
odir1 = odir1 + 'set_Pnorm_Pnow/'
if start_lmin != 1:
idir2 = idir2 + 'start_ell_{}/'.format(start_lmin)
odir1 = odir1 + 'start_ell_{}/'.format(start_lmin)
if args.modify_Cov_cij_cpq == 'True':
idir2 = idir2 + 'modify_Cov_cij_cpq/'
odir1 = odir1 + 'modify_Cov_cij_cpq/'
if params_str == '001':
odir1 = odir1 + 'alpha_{0:.2f}/'.format(args.alpha)
if f_sky:
idir = idir0 + idir1.format(
lt_prefix[lt], Pwig_type, f_sky
) + idir2 # not exactly matching format, but it's ok if there is no f_sky parameter.
else:
idir = idir0 + idir1.format(lt_prefix[lt], Pwig_type) + idir2
odir = idir0 + odir1
if rank == 0:
if not os.path.exists(odir):
os.makedirs(odir)
if args.save_sampler == 'True':
os.makedirs(
odir +
'chain_samplers/') # store positions of samplers in chains
comm.Barrier()
ifile = idir + 'Pk_wnw_{}rbin_{}kbin_withshapenoisefactor{}_{}eigenvW.out'.format(
num_rbin, num_kbin, shapenf, num_kbin)
k_all = np.loadtxt(ifile, dtype='f8', comments='#', usecols=(0, ))
indices = filter_krange(
k_all, kmin, kmax) # Here we don't need to use sigma_Pk_wnw anymore.
N_fitbin = len(indices)
print('# of fit k bins: ', N_fitbin)
print('The indices of fitting k bins: ', indices)
if set_SVc_on_CovP != 'True':
ifile = idir + 'Cov_Pwnw_inv_{}rbin_{}kbin_withshapenoisefactor{}.npz'.format(
num_rbin, num_kbin, shapenf)
npzfile = np.load(ifile)
icov_Pk_wnw = npzfile['arr_0']
print('icov_Pk_wnw: ', icov_Pk_wnw)
cov_Pwnw = linalg.inv(icov_Pk_wnw)
print('cov_Pwnw: ', cov_Pwnw)
identity = np.dot(cov_Pwnw, icov_Pk_wnw)
print('cov * icov: ', identity)
print('Inverse process is good?',
np.allclose(identity, np.eye(num_kbin))
) # test whether the inverse process is very successful
part_cov_Pwnw = cov_Pwnw[np.ix_(indices, indices)]
part_icov_Pk_wnw = linalg.inv(part_cov_Pwnw)
print(
'Inverse process for marginalized matrix is good?',
np.allclose(np.dot(part_cov_Pwnw, part_icov_Pk_wnw),
np.eye(N_fitbin)))
print('The inverse covariance matrix for fitting: ', part_icov_Pk_wnw)
pool = MPIPool(loadbalance=True)
for num_eigv in range(args.nSV_min, num_kbin + 1):
np.random.seed(1)
if f_sky:
idir_Pwig = idir0 + idir1.format(lt_prefix[lt], Pwig_type,
f_sky) + idir2
idir_Pnow = idir0 + idir1.format(lt_prefix[lt], 'Pnow',
f_sky) + idir2
else:
idir_Pwig = idir0 + idir1.format(lt_prefix[lt], Pwig_type) + idir2
idir_Pnow = idir0 + idir1.format(lt_prefix[lt], 'Pnow') + idir2
ifile = idir_Pwig + 'Pk_wig_{}rbin_{}kbin_withshapenoisefactor{}_{}eigenvW.out'.format(
num_rbin, num_kbin, shapenf, num_eigv)
print(ifile)
data_m = np.loadtxt(ifile, dtype='f8',
comments='#') # k, P(k), sigma_Pk
k_obs, Pk_wig_obs = data_m[indices, 0], data_m[indices, 1]
ifile = idir_Pnow + 'Pk_now_{}rbin_{}kbin_withshapenoisefactor{}_{}eigenvW.out'.format(
num_rbin, num_kbin, shapenf, num_eigv)
print(ifile)
data_m = np.loadtxt(ifile, dtype='f8', comments='#')
k_obs, Pk_now_obs = data_m[indices, 0], data_m[indices, 1]
Pk_wnw_obs = Pk_wig_obs / Pk_now_obs
if set_SVc_on_CovP == 'True':
ifile = idir_Pwig + 'Cov_Pwnw_inv_{}rbin_{}kbin_withshapenoisefactor{}_{}eigenvW_SVc.npz'.format(
num_rbin, num_kbin, shapenf, num_eigv)
####ifile = idir_Pwig + 'Cov_Pwnw_inv_{}rbin_{}kbin_withshapenoisefactor1.0_{}eigenvW_SVc.npz'.format(num_rbin, num_kbin, num_eigv) # only for some special case, it's temporary
part_icov_Pk_wnw = filter_invCov_on_k(ifile, indices)
mergedsamples, params_mcmc = mcmc_routine(N_params, N_walkers, theta,
params_T, params_indices,
fix_params, k_obs,
Pk_wnw_obs, part_icov_Pk_wnw,
Pwig_spl, Psm_spl, norm_gf,
params_name, pool)
print(params_mcmc)
chi_square = chi2(params_mcmc[:, 0], params_indices, fix_params, k_obs,
Pk_wnw_obs, part_icov_Pk_wnw, Pwig_spl, Psm_spl,
norm_gf)
dof = N_fitbin - N_params
reduced_chi2 = chi_square / dof
print("chi^2/dof: ", reduced_chi2, "\n")
if args.Sigma2_inf == 'True':
# in order to distinguish the Sigma2_xy value, we need to specify it.
filename = 'Pk_wnw_{}rbin_{}kbin_snf{}_{}eigenvW_params{}_Sigma2_{}.dat'.format(
num_rbin, num_kbin, shapenf, num_eigv, params_str, Sigma2_xy)
else:
filename = 'Pk_wnw_{}rbin_{}kbin_snf{}_{}eigenvW_params{}.dat'.format(
num_rbin, num_kbin, shapenf, num_eigv,
params_str) # Sigma2_xy is fixed in the default case
ofile_params = odir + filename
print('ofile_params:', ofile_params)
write_params(ofile_params, params_mcmc, params_name, reduced_chi2,
fix_params, dof)
if (args.save_sampler == 'True') and (rank == 0):
odir_merged_sample = odir + 'chain_samplers/'
if not os.path.exists(odir_merged_sample):
os.makedirs(odir_merged_sample)
ofile = odir_merged_sample + 'mergedsamples_' + filename[
0:len(filename) - 4] + '.npz'
np.savez_compressed(ofile, np.array(mergedsamples))
pool.close()
sys.stdout = old_stdout
log_file.close()
class EnsembleSampler(GenericSampler):
def __init__(self, num_walkers=None, num_steps=5000, num_burn=2000,
temp_dir=None, save_interval=300):
""" Uses ``emcee`` and the `EnsembleSampler
<http://dan.iel.fm/emcee/current/api/#emcee.EnsembleSampler>`_ to fit the supplied
model.
This method sets an emcee run using the ``EnsembleSampler`` and manual
chain management to allow for low to medium dimensional models. MPI running
is detected automatically for less hassle, and chain progress is serialised
to disk automatically for convenience.
Parameters
----------
num_walkers : int, optional
The number of walkers to run. If not supplied, it defaults to eight times the
framework dimensionality
num_steps : int, optional
The number of steps to run
num_burn : int, optional
The number of steps to discard for burn in
temp_dir : str
If set, specifies a directory in which to save temporary results, like the emcee chain
save_interval : float
The amount of seconds between saving the chain to file. Setting to ``None``
disables serialisation.
"""
self.logger = logging.getLogger(__name__)
import emcee
self.chain = None
self.pool = None
self.master = True
self.num_steps = num_steps
self.num_burn = num_burn
self.temp_dir = temp_dir
if temp_dir is not None and not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.save_interval = save_interval
self.num_walkers = num_walkers
def fit(self, kwargs):
""" Runs the sampler over the model and returns the flat chain of results
Parameters
----------
kwargs : dict
Containing the following information at a minimum:
- log_posterior : function
A function which takes a list of parameters and returns
the log posterior
- start : function|list|ndarray
Either a starting position, or a function that can be called
to generate a starting position
- save_dims : int, optional
Only return values for the first ``save_dims`` parameters.
Useful to remove numerous marginalisation parameters if running
low on memory or hard drive space.
- uid : str, optional
A unique identifier used to differentiate different fits
if two fits both serialise their chains and use the
same temporary directory
Returns
-------
dict
A dictionary with key "chains" containing the final
flattened chain of dimensions
``(num_dimensions, num_walkers * (num_steps - num_burn))``
"""
log_posterior = kwargs.get("log_posterior")
start = kwargs.get("start")
save_dims = kwargs.get("save_dims")
uid = kwargs.get("uid")
assert log_posterior is not None
assert start is not None
from emcee.utils import MPIPool
import emcee
try: # pragma: no cover
self.pool = MPIPool()
if not self.pool.is_master():
self.logger.info("Slave waiting")
self.master = False
self.pool.wait()
sys.exit(0)
else:
self.logger.info("MPIPool successful initialised and master found. "
"Running with %d cores." % self.pool.size)
except ImportError:
self.logger.info("mpi4py is not installed or not configured properly. "
"Ignore if running through python, not mpirun")
except ValueError as e: # pragma: no cover
self.logger.info("Unable to start MPI pool, expected normal python execution")
self.logger.info(str(e))
if callable(start):
num_dim = start().size
else:
num_dim = start.size
if self.num_walkers is None:
self.num_walkers = num_dim * 4
self.num_walkers = max(self.num_walkers, 20)
self.logger.debug("Fitting framework with %d dimensions" % num_dim)
self.logger.info("Using Ensemble Sampler")
sampler = emcee.EnsembleSampler(self.num_walkers, num_dim,
log_posterior,
pool=self.pool, live_dangerously=True)
emcee_wrapper = EmceeWrapper(sampler)
flat_chain = emcee_wrapper.run_chain(self.num_steps, self.num_burn,
self.num_walkers, num_dim,
start=start,
save_dim=save_dims,
temp_dir=self.temp_dir,
uid=uid,
save_interval=self.save_interval)
self.logger.debug("Fit finished")
if self.pool is not None: # pragma: no cover
self.pool.close()
self.logger.debug("Pool closed")
return {"chain": flat_chain}
def rerunPosteriorPredictive():
''' Rerun the posterior predictive distribution. This can be used to e.g. increase the resolution
spatially or in terms of the age of stellar populations, or vary some parameter systematically.
The mandatory argument func is a user-provided function that specifies how a model with known
parameters should be modified and (re) run.'''
pool = MPIPool(comm=comm, loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
output = readoutput.Experiment(chainDirRel+'-ppd') # read in the posterior predictive distribution.
output.read(paramsOnly=True,keepStars=False)
emcee_params = []
print "output.models: ",len(output.models)
# For each model, take the parameters we have read in and construct the corresponding emcee parameters.
for model in output.models:
#eta, epsff, fg0, muNorm, muMhScaling, fixedQ, accScaleLength, fcool, Mh0, fscatter, x0, x1, x2, x3, obsScale, conRF, muHgScaling = emceeParams
eta = model.p['eta']
epsff = model.p['epsff']
fg0 = model.p['fg0']
muNorm = model.p['muNorm']
muMhScaling = model.p['muMhScaling']
fixedQ = model.p['fixedQ']
accScaleLength = model.p['accScaleLength']
fcool = model.p['fcool']
Mh0 = model.p['Mh0']
fscatter = model.p['fscatter']
x0 = model.p['x0']
x1 = model.p['x1']
x2 = model.p['x2']
x3 = model.p['x3']
obsScale = 1.0 # doesn't matter.. see below
conRF = model.p['concentrationRandomFactor']
muHgScaling = model.p['muHgScaling']
# We have everything except obsScale, but actually that doesn't matter,
# since it only affects the model in post-processing, i.e. in comparing to the data,
# not the running of the model itself. So..... we good!
theList = [ eta, epsff, fg0, muNorm, muMhScaling, fixedQ, accScaleLength, fcool, Mh0, fscatter, x0, x1, x2, x3, obsScale, conRF, muHgScaling]
try:
assert eta>0 and epsff>0 and fg0>0 and fg0<=1 and fixedQ>0 and muNorm>=0 and fcool>=0 and fcool<=1 and Mh0>0
except:
print 'Unexpected ppd params: ',theList
emcee_params.append( copy.deepcopy(theList) )
# OK, from here on out, we just need to emulate parts of the run() function to trick emcee into running a single iteration of the algorithm with this IC.
ndim = 17
restart = {}
restart['currentPosition'] = emcee_params
restart['chain'] = None
restart['state'] = None
restart['prob'] = None
restart['iterationCounter'] = 0
restart['mcmcRunCounter'] = 0
nwalkers = len(emcee_params) # Need one walker per sample from posterior predictive distribution
print "Starting up the ensemble sampler!"
sampler = emcee.EnsembleSampler(nwalkers, ndim, fakeProb, pool=pool)
#pos, prob, state = sampler.run_mcmc(restart['currentPosition'], N, rstate0=restart['state'], lnprob0=restart['prob'])
print "Take a step with the ensemble sampler"
# Take a single step with the ensemble sampler.
print np.shape(restart['currentPosition']), np.shape(np.random.uniform(0,1,nwalkers))
sampler._get_lnprob(pos = restart['currentPosition'])
#result = sampler.sample(restart['currentPosition'], iterations=1, lnprob0=None, rstate0=None)
#pos, prob, state = result
print "Close the pool"
pool.close()
def main(runmpi=True, nw=100, th=6, bi=10, fr=10):
if runmpi:
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
else:
pool = None
#ldfileloc = '/Users/tom/Projects/koi2133/code/'
ldfileloc = '/nobackup/tsbarcl2/Projects/koi2133/code/'
#codedir = '/Users/tom/Projects/koi2133/code'
codedir = '/nobackup/tsbarcl2/Projects/koi2133/code'
koi = 2133
cadence = 1625.3
teff = 4550.
teff_unc = 75.
feh = 0.11
feh_unc = 0.07
logg = 2.943
logg_unc = 0.007
rho = 0.0073
rho_unc = 0.0001
nplanets = 1
dil = 0.0
period = 6.24672336
impact = 0.7
T0 = 136.383880
rprs = 0.02067
alb = 30.
occ = 40.
ell = 30.
rvamp = 79.0
ecosw = 0.048
esinw = -0.045
planet_guess = np.array(
[T0, period, impact, rprs, ecosw, esinw, rvamp, occ, ell, alb])
rvtime, rvval, rverr = get_rv()
time, flux, ferr = get_lc()
rho_prior = True
ldp_prior = False
nwalkers = nw
threads = th
burnin = bi
fullrun = fr
thin = 1
n_ldparams = 2
toffset_lc = 0
toffset_rv = 0
zpt_0 = 1.E-10
M = tmod.transitemcee_koi2133(nplanets,
cadence,
ldfileloc=ldfileloc,
codedir=codedir)
M.get_stellar(teff, logg, feh, n_ldparams, ldp_prior=ldp_prior)
M.already_open(time,
flux,
ferr,
rvtime,
rvval,
rverr,
timeoffset=toffset_lc,
rvtimeoffset=toffset_rv,
normalize=False)
rho_vals = np.array([rho, rho_unc])
M.get_rho(rho_vals, rho_prior)
M.get_zpt(zpt_0)
noise_model = [3.0E-4, 3.7E-2, 2.E-4, 3.]
if dil is not None:
M.get_sol(*planet_guess, dil=dil, noise_model=noise_model)
else:
M.get_sol(*planet_guess, noise_model=noise_model)
outfile = 'koi{0}_np{1}_prior{2}_dil{3}GP.hdf5'.format(
koi, nplanets, rho_prior, dil)
p0 = M.get_guess(nwalkers)
#dirty hack!!
qwe = np.r_[np.arange(0, 7), np.arange(9, 21)]
p0 = p0[:, qwe]
l_var = np.shape(p0)[1]
N = len([indval for indval in xrange(fullrun) if indval % thin == 0])
with h5py.File(outfile, u"w") as f:
f.create_dataset("time", data=M.time)
f.create_dataset("flux", data=M.flux)
f.create_dataset("err", data=M.err)
f.create_dataset("rvtime", data=M.rvtime)
f.create_dataset("rvval", data=M.rvval)
f.create_dataset("rverr", data=M.rverr)
f.create_dataset("itime", data=M._itime)
f.create_dataset("ntt", data=M._ntt)
f.create_dataset("tobs", data=M._tobs)
f.create_dataset("omc", data=M._omc)
f.create_dataset("datatype", data=M._datatype)
f.attrs["rho_0"] = M.rho_0
f.attrs["rho_0_unc"] = M.rho_0_unc
f.attrs["nplanets"] = M.nplanets
f.attrs["ld1"] = M.ld1
f.attrs["ld2"] = M.ld2
f.attrs["koi"] = koi
f.attrs["dil"] = dil
g = f.create_group("mcmc")
g.attrs["nwalkers"] = nwalkers
g.attrs["burnin"] = burnin
g.attrs["iterations"] = fullrun
g.attrs["thin"] = thin
g.attrs["rho_prior"] = rho_prior
g.attrs["ldp_prior"] = ldp_prior
g.attrs["onlytransits"] = M.onlytransits
g.attrs["tregion"] = M.tregion
g.attrs["ldfileloc"] = M.ldfileloc
g.attrs["n_ldparams"] = M.n_ldparams
g.create_dataset("fixed_sol", data=M.fixed_sol)
g.create_dataset("fit_sol_0", data=M.fit_sol_0)
c_ds = g.create_dataset("chain", (nwalkers, N, l_var),
dtype=np.float64)
lp_ds = g.create_dataset("lnprob", (nwalkers, N), dtype=np.float64)
#I don't like the default LDP unc
#I'm changing them
M.ld1_unc = 0.8
M.ld2_unc = 0.8
args = [
M.nplanets, M.rho_0, M.rho_0_unc, M.rho_prior, M.ld1, M.ld1_unc,
M.ld2, M.ld2_unc, M.ldp_prior, M.flux, M.err, M.fixed_sol, M.time,
M._itime, M._ntt, M._tobs, M._omc, M._datatype, M.rvtime, M.rvval,
M.rverr, M._rvitime, M.n_ldparams, M.ldfileloc, M.onlytransits,
M.tregion
]
tom = tmod.logchi2_rv_phaseGP2
if runmpi:
sampler = emcee.EnsembleSampler(nwalkers,
l_var,
tom,
args=args,
pool=pool)
else:
sampler = emcee.EnsembleSampler(nwalkers,
l_var,
tom,
args=args,
threads=th)
time1 = thetime.time()
p2, prob, state = sampler.run_mcmc(p0, burnin, storechain=False)
sampler.reset()
with h5py.File(outfile, u"a") as f:
g = f["mcmc"]
g.create_dataset("burnin_pos", data=p2)
g.create_dataset("burnin_prob", data=prob)
time2 = thetime.time()
print('burn-in took ' + str((time2 - time1) / 60.) + ' min')
time1 = thetime.time()
for i, (pos, lnprob, state) in enumerate(
sampler.sample(p2,
iterations=fullrun,
rstate0=state,
storechain=False)):
#do the thinning in the loop here
if i % thin == 0:
ind = i / thin
with h5py.File(outfile, u"a") as f:
g = f["mcmc"]
c_ds = g["chain"]
lp_ds = g["lnprob"]
c_ds[:, ind, :] = pos
lp_ds[:, ind] = lnprob
time2 = thetime.time()
print('MCMC run took ' + str((time2 - time1) / 60.) + ' min')
print('')
print("Mean acceptance: " + str(np.mean(sampler.acceptance_fraction)))
print('')
if runmpi:
pool.close()
else:
sampler.pool.close()
return sampler
def run(N, p00=None, nwalkers=500):
fn = chainDirRel+'.pickle'
ndim = 17
if p00 is not None:
p0 = [p00*(1.0+0.001*np.random.randn( ndim )) for i in range(nwalkers)]
else:
p0 = [sampleFromPrior() for i in range(nwalkers)]
restart = {}
restart['currentPosition'] = p0
restart['chain'] = None
restart['state'] = None
restart['prob'] = None
restart['iterationCounter'] = 0
restart['mcmcRunCounter'] = 0
# Read in our past progress UNLESS we've been given a new starting location.
if p00 is None:
updateRestart(fn,restart)
if restart['chain'] is not None:
# This may save some time if you change something and forget to delete the .pickle file.
restartedShape = np.shape(restart['chain'])
print restartedShape, nwalkers, ndim
assert restartedShape[0] == nwalkers
assert restartedShape[2] == ndim
global runNumber
runNumber = restart['mcmcRunCounter']
restart['iterationCounter'] += N
restart['mcmcRunCounter'] += 1
pool = MPIPool(comm=comm, loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnProb, pool=pool)
#pos, prob, state = sampler.run_mcmc(restart['currentPosition'], N, rstate0=restart['state'], lnprob0=restart['prob'])
for result in sampler.sample(restart['currentPosition'], iterations=N, lnprob0=restart['prob'], rstate0=restart['state']):
pos, prob, state = result
restart['acor'] = sampler.acor[:] # autocorr length for each param (ndim)
restart['accept'] = sampler.acceptance_fraction[:] # acceptance frac for each walker.
restart['currentPosition'] = pos # same shape as p0: nwalkers x ndim
restart['state'] = state # random number generator state
restart['prob'] = prob # nwalkers x __
if restart['chain'] is None:
restart['chain'] = np.expand_dims(sampler.chain[:,0,:],1) # nwalkers x niterations x ndim
restart['allProbs'] = np.expand_dims(prob,1) # nwalkers x niterations
else:
print np.shape(restart['chain']), np.shape(sampler.chain[:,-1,:]), np.shape(sampler.chain)
print restart['mcmcRunCounter'], restart['iterationCounter']
#restart['chain'] = np.concatenate((restart['chain'], sampler.chain[:,-1,:]), axis=1)
print "dbg1: ",np.shape(restart['chain']), np.shape(np.zeros((nwalkers, 1, ndim))), np.shape(np.expand_dims(pos,1))
restart['chain'] = np.concatenate((restart['chain'], np.expand_dims(pos, 1)),axis=1)
restart['allProbs'] = np.concatenate((restart['allProbs'], np.expand_dims(prob, 1)),axis=1)
saveRestart(fn,restart)
pool.close()
def main():
##################
#These change a lot
numWaveforms = 12
numThreads = 8
ndim = 6*numWaveforms + 7
nwalkers = 25*ndim
iter=10000
burnIn = 9000
######################
doPlots = 1
# plt.ion()
fitSamples = 350
timeStepSize = 1. #ns
#Prepare detector
tempGuess = 79.310080
gradGuess = 0.05
pcRadGuess = 2.5
pcLenGuess = 1.6
#Create a detector model
detName = "conf/P42574A_grad%0.2f_pcrad%0.2f_pclen%0.2f.conf" % (0.05,2.5, 1.65)
det = Detector(detName, temperature=tempGuess, timeStep=timeStepSize, numSteps=fitSamples*10 )
det.LoadFields("P42574A_fields_v3.npz")
det.SetFields(pcRadGuess, pcLenGuess, gradGuess)
b_over_a = 0.107213
c = -0.821158
d = 0.828957
rc1 = 74.4
rc2 = 1.79
rcfrac = 0.992
det.SetTransferFunction(b_over_a, c, d, rc1, rc2, rcfrac)
tempIdx = -7
#and the remaining 4 are for the transfer function
fig_size = (20,10)
#Create a decent start guess by fitting waveform-by-waveform
wfFileName = "P42574A_12_fastandslow_oldwfs.npz"
# wfFileName = "P42574A_5_fast.npz"
if os.path.isfile(wfFileName):
data = np.load(wfFileName)
results = data['results']
wfs = data['wfs']
# wfs = wfs[::3]
# results = results[::3]
numWaveforms = wfs.size
else:
print "No saved waveforms available. Exiting."
exit(0)
#prep holders for each wf-specific param
r_arr = np.empty(numWaveforms)
phi_arr = np.empty(numWaveforms)
z_arr = np.empty(numWaveforms)
scale_arr = np.empty(numWaveforms)
t0_arr = np.empty(numWaveforms)
smooth_arr = np.ones(numWaveforms)*7.
simWfArr = np.empty((1,numWaveforms, fitSamples))
#Prepare the initial value arrays
for (idx, wf) in enumerate(wfs):
wf.WindowWaveformTimepoint(fallPercentage=.97, rmsMult=2,)
r_arr[idx], phi_arr[idx], z_arr[idx], scale_arr[idx], t0_arr[idx], smooth_arr[idx] = results[idx]['x']
# t0_arr[idx] -= 15
#Initialize the multithreading
# p = Pool(numThreads, initializer=initializeDetectorAndWaveforms, initargs=[det, wfs])
initializeDetectorAndWaveforms(det, wfs)
p = MPIPool()
if not p.is_master():
p.wait()
sys.exit(0)
#Do the MCMC
mcmc_startguess = np.hstack((r_arr[:], phi_arr[:], z_arr[:], scale_arr[:], t0_arr[:], smooth_arr[:], # waveform-specific params
tempGuess, b_over_a, c, d, rc1, rc2, rcfrac)) # detector-specific
#number of walkers _must_ be even
if nwalkers % 2:
nwalkers +=1
pos0 = [mcmc_startguess + 1e-2*np.random.randn(ndim)*mcmc_startguess for i in range(nwalkers)]
rc1idx = -3
rc2idx = -2
rcfracidx = -1
#Make sure everything in the initial guess is within bounds
for pos in pos0:
pos[:numWaveforms] = np.clip( pos[:numWaveforms], 0, np.floor(det.detector_radius*10.)/10.)
pos[numWaveforms:2*numWaveforms] = np.clip(pos[numWaveforms:2*numWaveforms], 0, np.pi/4)
pos[2*numWaveforms:3*numWaveforms] = np.clip(pos[2*numWaveforms:3*numWaveforms], 0, np.floor(det.detector_length*10.)/10.)
pos[4*numWaveforms:5*numWaveforms] = np.clip(pos[4*numWaveforms:5*numWaveforms], 0, fitSamples)
pos[5*numWaveforms:6*numWaveforms] = np.clip(pos[5*numWaveforms:6*numWaveforms], 0, 20.)
pos[tempIdx] = np.clip(pos[tempIdx], 40, 120)
pos[rcfracidx] = np.clip(pos[rcfracidx], 0, 1)
pos[rc2idx] = np.clip(pos[rc2idx], 0, np.inf)
pos[rc1idx] = np.clip(pos[rc1idx], 0, np.inf)
prior = lnprior(pos,)
if not np.isfinite(prior) :
print "BAD PRIOR WITH START GUESS YOURE KILLING ME SMALLS"
print pos
exit(0)
#Initialize, run the MCMC
sampler = emcee.EnsembleSampler( nwalkers, ndim, lnprob, pool=p)
#w/ progress bar, & time the thing
bar = ProgressBar(widgets=[Percentage(), Bar(), ETA()], maxval=iter).start()
for (idx,result) in enumerate(sampler.sample(pos0, iterations=iter, storechain=True)):
bar.update(idx+1)
bar.finish()
p.close()
print "Dumping chain to file..."
np.save("mpisampler_%dwfs.npy" % numWaveforms, sampler.chain)
def main(argv):
##################
#These change a lot
numWaveforms = 16
numThreads = 12
ndim = 6*numWaveforms + 8
nwalkers = 2*ndim
iter=50
burnIn = 40
wfPlotNumber = 10
######################
# plt.ion()
fitSamples = 200
#Prepare detector
zero_1 = -5.56351644e+07
pole_1 = -1.38796386e+04
pole_real = -2.02559385e+07
pole_imag = 9885315.37450211
zeros = [zero_1,0 ]
poles = [ pole_real+pole_imag*1j, pole_real-pole_imag*1j, pole_1]
system = signal.lti(zeros, poles, 1E7 )
tempGuess = 77.89
gradGuess = 0.0483
pcRadGuess = 2.591182
pcLenGuess = 1.613357
#Create a detector model
detName = "conf/P42574A_grad%0.2f_pcrad%0.2f_pclen%0.2f.conf" % (0.05,2.5, 1.65)
det = Detector(detName, temperature=tempGuess, timeStep=1., numSteps=fitSamples*10, tfSystem=system)
det.LoadFields("P42574A_fields_v3.npz")
det.SetFields(pcRadGuess, pcLenGuess, gradGuess)
tempIdx = -8
gradIdx = -7
pcRadIdx = -6
pcLenIdx = -5
#and the remaining 4 are for the transfer function
fig_size = (20,10)
#Create a decent start guess by fitting waveform-by-waveform
wfFileName = "P42574A_512waveforms_%drisetimeculled.npz" % numWaveforms
if os.path.isfile(wfFileName):
data = np.load(wfFileName)
results = data['results']
wfs = data['wfs']
numWaveforms = wfs.size
else:
print "No saved waveforms available. Loading from Data"
exit(0)
#prep holders for each wf-specific param
r_arr = np.empty(numWaveforms)
phi_arr = np.empty(numWaveforms)
z_arr = np.empty(numWaveforms)
scale_arr = np.empty(numWaveforms)
t0_arr = np.empty(numWaveforms)
smooth_arr = np.ones(numWaveforms)*7.
simWfArr = np.empty((1,numWaveforms, fitSamples))
#Prepare the initial value arrays
for (idx, wf) in enumerate(wfs):
wf.WindowWaveformTimepoint(fallPercentage=.99)
r_arr[idx], phi_arr[idx], z_arr[idx], scale_arr[idx], t0_arr[idx], smooth_arr[idx] = results[idx]['x']
t0_arr[idx] += 10 #because i had a different windowing offset back in the day
#Plot the waveforms to take a look at the initial guesses
if False:
fig = plt.figure()
for (idx,wf) in enumerate(wfs):
print "WF number %d:" % idx
print " >>r: %f\n >>phi %f\n >>z %f\n >>e %f\n >>t0 %f\n >>smooth %f" % (r_arr[idx], phi_arr[idx], z_arr[idx], scale_arr[idx], t0_arr[idx], smooth_arr[idx])
ml_wf = det.GetSimWaveform(r_arr[idx], phi_arr[idx], z_arr[idx], scale_arr[idx]*100, t0_arr[idx], fitSamples, smoothing = smooth_arr[idx])
plt.plot(ml_wf, color="b")
plt.plot(wf.windowedWf, color="r")
value = raw_input(' --> Press q to quit, any other key to continue\n')
if value == 'q': exit(0)
#Initialize this thread's globals
initializeDetectorAndWaveforms(det, wfs)
#Initialize the multithreading
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
#Do the MCMC
mcmc_startguess = np.hstack((r_arr[:], phi_arr[:], z_arr[:], scale_arr[:]*100., t0_arr[:],smooth_arr[:], # waveform-specific params
tempGuess, gradGuess,pcRadGuess, pcLenGuess, zero_1, pole_1, pole_real, pole_imag)) # detector-specific
#number of walkers _must_ be even
if nwalkers % 2:
nwalkers +=1
#Initialize walkers with a random, narrow ball around the start guess
pos0 = [mcmc_startguess + 1e-2*np.random.randn(ndim)*mcmc_startguess for i in range(nwalkers)]
#Make sure everything in the initial guess is within bounds
for pos in pos0:
pos[:numWaveforms] = np.clip( pos[:numWaveforms], 0, np.floor(det.detector_radius*10.)/10.)
pos[numWaveforms:2*numWaveforms] = np.clip(pos[numWaveforms:2*numWaveforms], 0, np.pi/4)
pos[2*numWaveforms:3*numWaveforms] = np.clip(pos[2*numWaveforms:3*numWaveforms], 0, np.floor(det.detector_length*10.)/10.)
pos[4*numWaveforms:5*numWaveforms] = np.clip(pos[4*numWaveforms:5*numWaveforms], 0, fitSamples)
pos[5*numWaveforms:6*numWaveforms] = np.clip(pos[5*numWaveforms:6*numWaveforms], 0, 20.)
pos[tempIdx] = np.clip(pos[tempIdx], 40, 120)
pos[gradIdx] = np.clip(pos[gradIdx], det.gradList[0], det.gradList[-1])
pos[pcRadIdx] = np.clip(pos[pcRadIdx], det.pcRadList[0], det.pcRadList[-1])
pos[pcLenIdx] = np.clip(pos[pcLenIdx], det.pcLenList[0], det.pcLenList[-1])
prior = lnprior(pos,)
if not np.isfinite(prior) :
print "BAD PRIOR WITH START GUESS YOURE KILLING ME SMALLS"
print pos
exit(0)
#Initialize, run the MCMC
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, pool=p)
#w/ progress bar, & time the thing
start = timer()
for (idx,result) in enumerate(sampler.sample(pos0, iterations=iter, storechain=True)):
continue
end = timer()
pool.close()
print "Elapsed time: " + str(end-start)
print "Dumping chain to file..."
np.save("sampler_mpi_%dwfs.npy" % numWaveforms, sampler.chain)
print "Making MCMC steps figure..."
######### Plots for Waveform params
stepsFig = plt.figure(2, figsize=fig_size)
plt.clf()
ax0 = stepsFig.add_subplot(611)
ax1 = stepsFig.add_subplot(612, sharex=ax0)
ax2 = stepsFig.add_subplot(613, sharex=ax0)
ax3 = stepsFig.add_subplot(614, sharex=ax0)
ax4 = stepsFig.add_subplot(615, sharex=ax0)
ax5 = stepsFig.add_subplot(616, sharex=ax0)
ax0.set_ylabel('r')
ax1.set_ylabel('phi')
ax2.set_ylabel('z')
ax3.set_ylabel('scale')
ax4.set_ylabel('t0')
ax5.set_ylabel('smoothing')
for i in range(nwalkers):
for j in range(wfs.size):
ax0.plot(sampler.chain[i,:,0+j], alpha=0.3) # r
ax1.plot(sampler.chain[i,:,numWaveforms + j], alpha=0.3) # phi
ax2.plot(sampler.chain[i,:,2*numWaveforms + j], alpha=0.3) #z
ax3.plot(sampler.chain[i,:,3*numWaveforms + j], alpha=0.3) #energy
ax4.plot(sampler.chain[i,:,4*numWaveforms + j], alpha=0.3) #t0
ax5.plot(sampler.chain[i,:,5*numWaveforms + j], alpha=0.3) #smoothing
plt.savefig("emcee_mpi_wfchain_%dwfs.png" % numWaveforms)
######### Plots for Detector params
stepsFigDet = plt.figure(3, figsize=fig_size)
plt.clf()
ax0 = stepsFigDet.add_subplot(411)
ax1 = stepsFigDet.add_subplot(412, sharex=ax0)
ax2 = stepsFigDet.add_subplot(413, sharex=ax0)
ax3 = stepsFigDet.add_subplot(414, sharex=ax0)
ax0.set_ylabel('temp')
ax1.set_ylabel('grad')
ax2.set_ylabel('pcRad')
ax3.set_ylabel('pcLen')
for i in range(nwalkers):
ax0.plot(sampler.chain[i,:,tempIdx], "b", alpha=0.3) #temp
ax1.plot(sampler.chain[i,:,gradIdx], "b", alpha=0.3) #grad
ax2.plot(sampler.chain[i,:,pcRadIdx], "b", alpha=0.3) #pcrad
ax3.plot(sampler.chain[i,:,pcLenIdx], "b", alpha=0.3) #pclen
plt.savefig("emcee_mpi_detchain_%dwfs.png" % numWaveforms)
#and for the transfer function
stepsFigTF = plt.figure(4, figsize=fig_size)
plt.clf()
tf0 = stepsFigTF.add_subplot(411)
tf1 = stepsFigTF.add_subplot(412, sharex=ax0)
tf2 = stepsFigTF.add_subplot(413, sharex=ax0)
tf3 = stepsFigTF.add_subplot(414, sharex=ax0)
tf0.set_ylabel('zero_1')
tf1.set_ylabel('pole_1')
tf2.set_ylabel('pole_real')
tf3.set_ylabel('pole_imag')
for i in range(nwalkers):
tf0.plot(sampler.chain[i,:,-4], "b", alpha=0.3) #2
tf1.plot(sampler.chain[i,:,-3], "b", alpha=0.3) #den1
tf2.plot(sampler.chain[i,:,-2], "b", alpha=0.3) #2
tf3.plot(sampler.chain[i,:,-1], "b", alpha=0.3) #3
plt.savefig("emcee_mpi_tfchain_%dwfs.png" % numWaveforms)
samples = sampler.chain[:, burnIn:, :].reshape((-1, ndim))
print "temp is %f" % np.median(samples[:,tempIdx])
print "grad is %f" % np.median(samples[:,gradIdx])
print "pcrad is %f" % np.median(samples[:,pcRadIdx])
print "pclen is %f" % np.median(samples[:,pcLenIdx])
print "zero_1 is %f" % np.median(samples[:,-4])
print "pole_1 is %f" % np.median(samples[:,-3])
print "pole_real is %f" % np.median(samples[:,-2])
print "pole_imag is %f" % np.median(samples[:,-1])
#TODO: Aaaaaaand plot some waveforms..
simWfs = np.empty((wfPlotNumber,numWaveforms, fitSamples))
for idx, (theta) in enumerate(samples[np.random.randint(len(samples), size=wfPlotNumber)]):
temp, impGrad, pcRad, pcLen = theta[tempIdx], theta[gradIdx], theta[pcRadIdx], theta[pcLenIdx]
zero_1, pole_1, pole_real, pole_imag = theta[-4:]
r_arr, phi_arr, z_arr, scale_arr, t0_arr, smooth_arr = theta[:-8].reshape((6, numWaveforms))
det.SetTemperature(temp)
det.SetFields(pcRad, pcLen, impGrad)
zeros = [zero_1,0 ]
poles = [ pole_real+pole_imag*1j, pole_real-pole_imag*1j, pole_1]
det.SetTransferFunction(zeros, poles, 1E7)
for wf_idx in range(wfs.size):
wf_i = det.GetSimWaveform(r_arr[wf_idx], phi_arr[wf_idx], z_arr[wf_idx], scale_arr[wf_idx], t0_arr[wf_idx], fitSamples)
simWfs[idx, wf_idx, :] = wf_i
if wf_i is None:
print "Waveform %d, %d is None" % (idx, wf_idx)
residFig = plt.figure(4, figsize=(20, 15))
helpers.plotManyResidual(simWfs, wfs, figure=residFig)
plt.savefig("emcee_mpi_waveforms_%dwfs.png" % numWaveforms)
def fit_subsamplefof_mean():
parser = argparse.ArgumentParser(
description=
'This is the MCMC code to get the fitting parameters, made by Zhejie Ding.'
)
parser.add_argument(
'-rec_id',
"--rec_id",
help='The id of reconstruction, either 0 or 1.',
required=True) #0: pre-reconstruct; 1: post-reconstruct
parser.add_argument(
'-space_id',
"--space_id",
help=
'The type of space for fitting, 0 for real-space and 1 for redshift space.',
required=True)
args = parser.parse_args()
print("args: ", args)
rec_id = int(args.rec_id)
print("rec_id: ", rec_id)
space_id = int(args.space_id)
print("space_id: ", space_id)
N_walkers = 40
# simulation run name
N_dataset = 20
N_mu_bin = 100
#N_skip_header = 11
#N_skip_footer = 31977
Omega_m = 0.3075
G_0 = growth_factor(0.0, Omega_m) # G_0 at z=0, normalization factor
Volume = 1380.0**3.0 # the volume of simulation box
sim_z = ['0', '0.6', '1.0']
sim_seed = [0, 9]
sim_wig = ['NW', 'WG']
sim_a = ['1.0000', '0.6250', '0.5000']
sim_space = ['r', 's'] # r for real space; s for redshift space
rec_dirs = [
'DD', 'ALL'
] # "ALL" folder stores P(k, \mu) after reconstruction process, while DD is before reconstruction.
rec_fprefix = ['', 'R']
mcut_Npar_list = [[37, 149, 516, 1524, 3830], [35, 123, 374, 962, 2105],
[34, 103, 290, 681, 1390]]
N_masscut = np.size(mcut_Npar_list, axis=1)
inputf = '../Zvonimir_data/planck_camb_56106182_matterpower_smooth_z0.dat'
k_smooth, Pk_smooth = np.loadtxt(inputf,
dtype='f8',
comments='#',
unpack=True)
tck_Pk_sm = interpolate.splrep(k_smooth, Pk_smooth)
inputf = '../Zvonimir_data/planck_camb_56106182_matterpower_z0.dat'
k_wiggle, Pk_wiggle = np.loadtxt(inputf,
dtype='f8',
comments='#',
unpack=True)
tck_Pk_linw = interpolate.splrep(k_wiggle, Pk_wiggle)
# firstly, read one file and get k bins we want for the fitting range
dir0 = '/Users/ding/Documents/playground/WiggleNowiggle/subsample_FoF_data_HS/Pk_obs_2d_wnw_mean_DD_ksorted_mu_masscut/'
inputf = dir0 + 'fof_kaver.wnw_diff_a_0.6250_mcut35_fraction0.126.dat'
k_p, mu_p = np.loadtxt(inputf,
dtype='f8',
comments='#',
delimiter=' ',
usecols=(0, 1),
unpack=True)
#print(k_p, mu_p)
N_fitbin = len(k_p)
#print('# of (k, mu) bins: ', N_fitbin)
# for output parameters fitted
odir = './ZV_lagrange_params_{}_wig-now_mean_dset/'.format(
rec_dirs[rec_id])
if not os.path.exists(odir):
os.makedirs(odir)
#space_id = 1 # in redshift space
if rec_id == 0:
##Sigma_0 = 8.3364 # the approximated value of \Sigma_xy and \Sigma_z, unit Mpc/h, at z=0.
Sigma_0 = 7.8364 # suggested by Zvonimir, at z=0
elif rec_id == 1:
Sigma_0 = 2.84
# 0: parameter fixed, 1: parameter free.
#params_indices = [1, 1, 1, 1, 1, 1, 0, 0] # Only for DM case. b0 needs to be fixed for DM subsample power spectrum. For this case, make sure \Sigma_xy and \Sigma_z positive, which should be set in mcmc_routine.
if space_id == 0:
# It may not work in real-space just setting f=0.
params_indices = [1, 1, 1, 0, 1, 1] # Set f=0 for real-space.
f = 0.0
elif space_id == 1:
params_indices = [1, 1, 1, 1, 1, 1] # for redshift space
f = 1.0
print("params_indices: ", params_indices)
alpha_1, alpha_2, sigma, b_0, b_scale = 1.0, 1.0, Sigma_0, 1.0, 0.0
all_names = "alpha_1", "alpha_2", "Sigma_qmax", "f", "b_1", "b_partial" # the same order for params_indices
all_temperature = 0.01, 0.01, 0.1, 0.1, 0.01, 0.1
pool = MPIPool(loadbalance=True)
for z_id in xrange(3):
norm_gf = growth_factor(float(sim_z[z_id]), Omega_m) / G_0
# ##Sigma_z = Sigma_0* norm_gf
#
# if set_Sigma_xyz_theory == "True":
# print("Sigma_z: ", Sigma_z)
# sigma_xy, sigma_z = Sigma_z, Sigma_z
# else:
# if params_indices[2] == 0:
# sigma_xy = 0.0
# else:
# sigma_xy = 10.0
# if params_indices[3] == 0:
# sigma_z = 0.0
# else:
# sigma_z = 10.0
all_params = alpha_1, alpha_2, sigma, f, b_0, b_scale
np.random.seed()
for mcut_id in xrange(N_masscut):
N_params, theta, fix_params, params_T, params_name = set_params(
all_params, params_indices, all_names, all_temperature)
ifile_Pk = './run2_3_Pk_obs_2d_wnw_mean_{}_ksorted_mu_masscut/{}kave{}.wig_minus_now_mean_fof_a_{}_mcut{}.dat'.format(
rec_dirs[rec_id], rec_fprefix[rec_id], sim_space[space_id],
sim_a[z_id], mcut_Npar_list[z_id][mcut_id])
Pk_wnw_diff_obs = np.loadtxt(
ifile_Pk, dtype='f4', comments='#', usecols=(2, )
) # be careful that there are k, \mu, P(k, \mu) columns.
ifile_Cov_Pk = './run2_3_Cov_Pk_obs_2d_wnw_{}_ksorted_mu_masscut/{}kave{}.wig_minus_now_mean_fof_a_{}_mcut{}.dat'.format(
rec_dirs[rec_id], rec_fprefix[rec_id], sim_space[space_id],
sim_a[z_id], mcut_Npar_list[z_id][mcut_id])
Cov_Pk_wnw = np.loadtxt(ifile_Cov_Pk, dtype='f4', comments='#')
ivar_Pk_wnow = N_dataset / np.diag(
Cov_Pk_wnw) # the mean sigma error
params_mcmc = mcmc_routine(N_params, N_walkers, theta, params_T,
params_indices, fix_params, k_p, mu_p,
Pk_wnw_diff_obs, ivar_Pk_wnow,
tck_Pk_linw, tck_Pk_sm, norm_gf,
params_name, pool)
chi_square = chi2(params_mcmc[:, 0], params_indices, fix_params,
k_p, mu_p, Pk_wnw_diff_obs, ivar_Pk_wnow,
tck_Pk_linw, tck_Pk_sm, norm_gf)
reduced_chi2 = chi_square / (N_fitbin - N_params)
print("Reduced chi2: {}\n".format(reduced_chi2))
# output parameters into a file
ofile_params = odir + 'fof_{}kave{}.wnw_diff_a_{}_mcut{}_params{}.dat'.format(
rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id],
mcut_Npar_list[z_id][mcut_id], ''.join(map(
str, params_indices)))
print(ofile_params)
write_params(ofile_params, params_mcmc, params_name, reduced_chi2)
np.random.seed()
N_params, theta, fix_params, params_T, params_name = set_params(
all_params, params_indices, all_names, all_temperature)
# Fit for DM power spectrum
ifile_Pk = './run2_3_sub_Pk_2d_wnw_mean_{}_ksorted_mu/{}kave{}.wig_minus_now_mean_sub_a_{}.dat'.format(
rec_dirs[rec_id], rec_fprefix[rec_id], sim_space[space_id],
sim_a[z_id])
Pk_wnw_diff_true = np.loadtxt(
ifile_Pk, dtype='f4', comments='#', usecols=(
2, )) # be careful that there are k, \mu, P(k, \mu) columns.
print(ifile_Pk)
ifile_Cov_Pk = './run2_3_sub_Cov_Pk_2d_wnw_{}_ksorted_mu/{}kave{}.wig_minus_now_mean_sub_a_{}.dat'.format(
rec_dirs[rec_id], rec_fprefix[rec_id], sim_space[space_id],
sim_a[z_id])
Cov_Pk_wnw = np.loadtxt(ifile_Cov_Pk, dtype='f4', comments='#')
ivar_Pk_wnow = N_dataset / np.diag(Cov_Pk_wnw) # the mean sigma error
params_mcmc = mcmc_routine(N_params, N_walkers, theta, params_T,
params_indices, fix_params, k_p, mu_p,
Pk_wnw_diff_true, ivar_Pk_wnow, tck_Pk_linw,
tck_Pk_sm, norm_gf, params_name, pool)
chi_square = chi2(params_mcmc[:, 0], params_indices, fix_params, k_p,
mu_p, Pk_wnw_diff_true, ivar_Pk_wnow, tck_Pk_linw,
tck_Pk_sm, norm_gf)
reduced_chi2 = chi_square / (N_fitbin - N_params)
print('Reduced chi2: {}\n'.format(reduced_chi2))
ofile_params = odir + 'sub_{}kave{}.wnw_diff_a_{}_params{}.dat'.format(
rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id], ''.join(
map(str, params_indices)))
write_params(ofile_params, params_mcmc, params_name, reduced_chi2)
pool.close()
def run_espei(run_settings):
"""Wrapper around the ESPEI fitting procedure, taking only a settings dictionary.
Parameters
----------
run_settings : dict
Dictionary of input settings
Returns
-------
Either a Database (for generate parameters only) or a tuple of (Database, sampler)
"""
run_settings = get_run_settings(run_settings)
system_settings = run_settings['system']
output_settings = run_settings['output']
generate_parameters_settings = run_settings.get('generate_parameters')
mcmc_settings = run_settings.get('mcmc')
# handle verbosity
verbosity = {0: logging.WARNING, 1: logging.INFO, 2: logging.DEBUG}
logging.basicConfig(level=verbosity[output_settings['verbosity']])
# load datasets and handle i/o
logging.debug('Loading and checking datasets.')
dataset_path = system_settings['datasets']
datasets = load_datasets(sorted(recursive_glob(dataset_path, '*.json')))
if len(datasets.all()) == 0:
logging.warning(
'No datasets were found in the path {}. This should be a directory containing dataset files ending in `.json`.'
.format(dataset_path))
logging.debug('Finished checking datasets')
with open(system_settings['phase_models']) as fp:
phase_models = json.load(fp)
if generate_parameters_settings is not None:
refdata = generate_parameters_settings['ref_state']
excess_model = generate_parameters_settings['excess_model']
dbf = generate_parameters(phase_models, datasets, refdata,
excess_model)
dbf.to_file(output_settings['output_db'], if_exists='overwrite')
if mcmc_settings is not None:
tracefile = output_settings['tracefile']
probfile = output_settings['probfile']
# check that the MCMC output files do not already exist
# only matters if we are actually running MCMC
if os.path.exists(tracefile):
raise OSError(
'Tracefile "{}" exists and would be overwritten by a new run. Use the ``output.tracefile`` setting to set a different name.'
.format(tracefile))
if os.path.exists(probfile):
raise OSError(
'Probfile "{}" exists and would be overwritten by a new run. Use the ``output.probfile`` setting to set a different name.'
.format(probfile))
# scheduler setup
if mcmc_settings['scheduler'] == 'MPIPool':
# check that cores is not an input setting
if mcmc_settings.get('cores') != None:
logging.warning("MPI does not take the cores input setting.")
from emcee.utils import MPIPool
# code recommended by emcee: if not master, wait for instructions then exit
client = MPIPool()
if not client.is_master():
logging.debug(
'MPIPool is not master. Waiting for instructions...')
client.wait()
sys.exit(0)
logging.info("Using MPIPool on {} MPI ranks".format(client.size))
elif mcmc_settings['scheduler'] == 'dask':
from distributed import LocalCluster
cores = mcmc_settings.get('cores', multiprocessing.cpu_count())
if (cores > multiprocessing.cpu_count()):
cores = multiprocessing.cpu_count()
logging.warning(
"The number of cores chosen is larger than available. "
"Defaulting to run on the {} available cores.".format(
cores))
scheduler = LocalCluster(n_workers=cores,
threads_per_worker=1,
processes=True)
client = ImmediateClient(scheduler)
client.run(logging.basicConfig,
level=verbosity[output_settings['verbosity']])
logging.info("Running with dask scheduler: %s [%s cores]" %
(scheduler, sum(client.ncores().values())))
try:
logging.info(
"bokeh server for dask scheduler at localhost:{}".format(
client.scheduler_info()['services']['bokeh']))
except KeyError:
logging.info("Install bokeh to use the dask bokeh server.")
elif mcmc_settings['scheduler'] == 'emcee':
from emcee.interruptible_pool import InterruptiblePool
cores = mcmc_settings.get('cores', multiprocessing.cpu_count())
if (cores > multiprocessing.cpu_count()):
cores = multiprocessing.cpu_count()
logging.warning(
"The number of cores chosen is larger than available. "
"Defaulting to run on the {} available cores.".format(
cores))
client = InterruptiblePool(processes=cores)
logging.info("Using multiprocessing on {} cores".format(cores))
elif mcmc_settings['scheduler'] == 'None':
client = None
logging.info(
"Not using a parallel scheduler. ESPEI is running MCMC on a single core."
)
# get a Database
if mcmc_settings.get('input_db'):
dbf = Database(mcmc_settings.get('input_db'))
# load the restart chain if needed
if mcmc_settings.get('restart_chain'):
restart_chain = np.load(mcmc_settings.get('restart_chain'))
else:
restart_chain = None
# load the remaning mcmc fitting parameters
mcmc_steps = mcmc_settings.get('mcmc_steps')
save_interval = mcmc_settings.get('mcmc_save_interval')
chains_per_parameter = mcmc_settings.get('chains_per_parameter')
chain_std_deviation = mcmc_settings.get('chain_std_deviation')
deterministic = mcmc_settings.get('deterministic')
dbf, sampler = mcmc_fit(
dbf,
datasets,
scheduler=client,
mcmc_steps=mcmc_steps,
chains_per_parameter=chains_per_parameter,
chain_std_deviation=chain_std_deviation,
save_interval=save_interval,
tracefile=tracefile,
probfile=probfile,
restart_chain=restart_chain,
deterministic=deterministic,
)
dbf.to_file(output_settings['output_db'], if_exists='overwrite')
# close the scheduler, if possible
if hasattr(client, 'close'):
client.close()
return dbf, sampler
return dbf
def fit_subsamplefof_mean():
parser = argparse.ArgumentParser(
description=
'This is the MCMC code to get the fitting parameters, made by Zhejie Ding.'
)
parser.add_argument(
'-rec_id',
"--rec_id",
help='The id of reconstruction, either 0 or 1.',
required=True) #0: pre-reconstruct; 1: post-reconstruct
parser.add_argument('-space_id',
"--space_id",
help='0 for real space, 1 for redshift space.',
required=True)
parser.add_argument(
'-set_Sigma_xyz_theory',
"--set_Sigma_xyz_theory",
help=
'Determine whether the parameters \Sigma_xy and \Sigma_z are fixed or not, either True or False',
required=True)
parser.add_argument(
'-set_Sigma_sm_theory',
"--set_Sigma_sm_theory",
help=
'Determine whether we use sigma_sm from theory in the fitting model. \
If False, sigma_sm=0 (be careful that sigma_sm=\inf in real space case)',
required=True)
args = parser.parse_args()
print("args: ", args)
rec_id = int(args.rec_id)
space_id = int(args.space_id)
set_Sigma_xyz_theory = args.set_Sigma_xyz_theory
set_Sigma_sm_theory = args.set_Sigma_sm_theory
print("rec_id: ", rec_id, "space_id: ", space_id)
print("set_Sigma_xyz_theory: ", set_Sigma_xyz_theory,
"set_Sigma_sm_theory: ", set_Sigma_sm_theory)
N_walkers = 40 # increase N_walkers would decrease the minimum number of walk steps which make fitting parameters convergent, but running time increases.
N_walkersteps = 5000
# simulation run name
N_dataset = 20
N_mu_bin = 100
#N_skip_header = 11
#N_skip_footer = 31977
Omega_m = 0.3075
G_0 = growth_factor(0.0, Omega_m) # G_0 at z=0, normalization factor
Volume = 1380.0**3.0 # the volume of simulation box
sim_z = ['0', '0.6', '1.0']
sim_seed = [0, 9]
sim_wig = ['NW', 'WG']
sim_a = ['1.0000', '0.6250', '0.5000']
sim_space = ['r', 's'] # r for real space; s for redshift space
rec_dirs = [
'DD', 'ALL'
] # "ALL" folder stores P(k, \mu) after reconstruction process, while DD is before reconstruction.
rec_fprefix = ['', 'R']
mcut_Npar_list = [[37, 149, 516, 1524, 3830], [35, 123, 374, 962, 2105],
[34, 103, 290, 681, 1390]]
N_masscut = np.size(mcut_Npar_list, axis=1)
# Sigma_sm = sqrt(2.* Sig_RR) in post-reconstruction case, for pre-reconstruction, we don't use sub_Sigma_RR.
Sigma_RR_list = [[37, 48.5, 65.5, 84.2, 110], [33, 38, 48.5, 63.5, 91.5],
[31, 38, 49, 65, 86]]
sub_Sigma_RR = 50.0 # note from Hee-Jong's recording
inputf = '../Zvonimir_data/planck_camb_56106182_matterpower_smooth_z0.dat'
k_smooth, Pk_smooth = np.loadtxt(inputf,
dtype='f8',
comments='#',
unpack=True)
tck_Pk_sm = interpolate.splrep(k_smooth, Pk_smooth)
inputf = '../Zvonimir_data/planck_camb_56106182_matterpower_z0.dat'
k_wiggle, Pk_wiggle = np.loadtxt(inputf,
dtype='f8',
comments='#',
unpack=True)
tck_Pk_linw = interpolate.splrep(k_wiggle, Pk_wiggle)
# firstly, read one file and get k bins we want for the fitting range
dir0 = '/Users/ding/Documents/playground/WiggleNowiggle/subsample_FoF_data_HS/Pk_obs_2d_wnw_mean_DD_ksorted_mu_masscut/'
inputf = dir0 + 'fof_kaver.wnw_diff_a_0.6250_mcut35_fraction0.126.dat'
k_p, mu_p = np.loadtxt(inputf,
dtype='f8',
comments='#',
delimiter=' ',
usecols=(0, 1),
unpack=True)
#print(k_p, mu_p)
N_fitbin = len(k_p)
#print('# of (k, mu) bins: ', N_fitbin)
# for output parameters fitted
odir = './params_{}_wig-now_b_bscale_fitted_mean_dset/'.format(
rec_dirs[rec_id])
if not os.path.exists(odir):
os.makedirs(odir)
print("N_walkers: ", N_walkers, "N_walkersteps: ", N_walkersteps, "\n")
if rec_id == 0:
##Sigma_0 = 8.3364 # the approximated value of \Sigma_xy and \Sigma_z, unit Mpc/h, at z=0.
Sigma_0 = 7.8364 # suggested by Zvonimir, at z=0
elif rec_id == 1:
Sigma_0 = 2.84
##space_id = 1 # in redshift space
# 0: parameter fixed, 1: parameter free.
#params_indices = [1, 1, 1, 1, 1, 1] # It doesn't fit \Sigma and bscale well. Yes, it dosen't work well (it's kind of overfitting).
##params_indices = [1, 1, 1, 1, 0, 1, 1, 0, 0] # b0 needs to be fitted. For this case, make sure \Sigma_xy and \Sigma_z positive, which should be set in mcmc_routine.
##params_indices = [0, 1, 0, 1, 1, 0] # make sure \alpha_xy = \alpha_z and \Sigma_xy = \Sigma_z
params_indices = [
1, 1, 1, 1, 0, 0, 0, 0, 0
] # Set sigma_fog=0, f=0, b_scale=0, b_0=1.0 for subsamled DM case in real space.
##params_indices = [1, 1, 0, 0, 1, 1] # with fixed Sigma from theoretical value, then need to set sigma_xy, sigma_z equal to Sigma_z
##params_indices = [0, 1, 0, 0, 1, 1] # For this case, make sure \alpha_1 = \alpha_2 in the function lnlike(..) and set sigma_xy, sigma_z equal to Sigma_z.
print("params_indices: ", params_indices)
##alpha_1, alpha_2, sigma_fog, f, b_0, b_scale = 1.0, 1.0, 2.0, 0.2, 1.0, 0.0
alpha_1, alpha_2, sigma_fog, f, b_0, b_scale = 1.0, 1.0, 0.0, 0.0, 1.0, 0.0 # ! only for real space, i.e., set sigma_fog, f equal to 0.
all_names = "alpha_1", "alpha_2", "sigma_xy", "sigma_z", "sigma_sm", "sigma_fog", "f", "b_0", "b_scale" # the same order for params_indices
all_temperature = 0.01, 0.01, 0.1, 0.1, 0.1, 0.1, 0.1, 0.01, 0.1
pool = MPIPool(loadbalance=True)
for z_id in xrange(3):
norm_gf = growth_factor(float(sim_z[z_id]), Omega_m) / G_0
Sigma_z = Sigma_0 * norm_gf / 2.0 # divided by 2.0 for estimated \Sigma of post-reconstruction
##Sigma_z = Sigma_0* norm_gf
if set_Sigma_xyz_theory == "True":
print("Sigma_z: ", Sigma_z)
sigma_xy, sigma_z = Sigma_z, Sigma_z
else:
if params_indices[2] == 0:
sigma_xy = 0.0
else:
sigma_xy = 10.0
if params_indices[3] == 0:
sigma_z = 0.0
else:
sigma_z = 10.0
np.random.seed()
# Set it for FoF fitting
# for mcut_id in xrange(N_masscut):
# if set_Sigma_sm_theory == "True":
# sigma_sm = (float(Sigma_RR_list[z_id][mcut_id])*2.0)**0.5
# else:
# sigma_sm = 0.0
#
# all_params = alpha_1, alpha_2, sigma_xy, sigma_z, sigma_sm, sigma_fog, f, b_0, b_scale
# N_params, theta, fix_params, params_T, params_name = set_params(all_params, params_indices, all_names, all_temperature)
#
# ifile_Pk = './run2_3_Pk_obs_2d_wnw_mean_{}_ksorted_mu_masscut/{}kave{}.wig_minus_now_mean_fof_a_{}_mcut{}.dat'.format(rec_dirs[rec_id], rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id], mcut_Npar_list[z_id][mcut_id])
# Pk_wnw_diff_obs = np.loadtxt(ifile_Pk, dtype='f4', comments='#', usecols=(2,)) # be careful that there are k, \mu, P(k, \mu) columns.
#
# ifile_Cov_Pk = './run2_3_Cov_Pk_obs_2d_wnw_{}_ksorted_mu_masscut/{}kave{}.wig_minus_now_mean_fof_a_{}_mcut{}.dat'.format(rec_dirs[rec_id], rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id], mcut_Npar_list[z_id][mcut_id])
# Cov_Pk_wnw = np.loadtxt(ifile_Cov_Pk, dtype='f4', comments='#')
# ivar_Pk_wnow = N_dataset/np.diag(Cov_Pk_wnw) # the mean sigma error
#
# params_mcmc = mcmc_routine(N_params, N_walkers, N_walkersteps, theta, params_T, params_indices, fix_params, k_p, mu_p, Pk_wnw_diff_obs, ivar_Pk_wnow, tck_Pk_linw, tck_Pk_sm, norm_gf, params_name, pool)
#
# chi_square = chi2(params_mcmc[:, 0], params_indices, fix_params, k_p, mu_p, Pk_wnw_diff_obs, ivar_Pk_wnow, tck_Pk_linw, tck_Pk_sm, norm_gf)
# reduced_chi2 = chi_square/(N_fitbin-N_params)
# print("Reduced chi2: {}\n".format(reduced_chi2))
# # output parameters into a file
# if set_Sigma_xyz_theory == "False":
# ofile_params = odir + 'fof_{}kave{}.wnw_diff_a_{}_mcut{}_params{}_Sigma_sm{}.dat'.format(rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id], mcut_Npar_list[z_id][mcut_id], ''.join(map(str, params_indices)), round(sigma_sm,3))
# else:
# ofile_params = odir + 'fof_{}kave{}.wnw_diff_a_{}_mcut{}_params{}_isotropic_Sigmaz_{}_Sigma_sm{}.dat'.format(rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id], mcut_Npar_list[z_id][mcut_id], ''.join(map(str, params_indices)), round(Sigma_z, 3), round(sigma_sm,3))
# print(ofile_params)
# write_params(ofile_params, params_mcmc, params_name, reduced_chi2)
# set it for DM subsample fitting
sub_sigma_sm = (sub_Sigma_RR * 2.0)**0.5
print("sub_sigma_sm: ", sub_sigma_sm)
all_params = alpha_1, alpha_2, sigma_xy, sigma_z, sub_sigma_sm, sigma_fog, f, b_0, b_scale # set \Sigma_sm = sqrt(50*2)=10, for post-rec
N_params, theta, fix_params, params_T, params_name = set_params(
all_params, params_indices, all_names, all_temperature)
# Fit for DM power spectrum
ifile_Pk = './run2_3_sub_Pk_2d_wnw_mean_{}_ksorted_mu/{}kave{}.wig_minus_now_mean_sub_a_{}.dat'.format(
rec_dirs[rec_id], rec_fprefix[rec_id], sim_space[space_id],
sim_a[z_id])
Pk_wnw_diff_true = np.loadtxt(
ifile_Pk, dtype='f4', comments='#', usecols=(
2, )) # be careful that there are k, \mu, P(k, \mu) columns.
ifile_Cov_Pk = './run2_3_sub_Cov_Pk_2d_wnw_{}_ksorted_mu/{}kave{}.wig_minus_now_mean_sub_a_{}.dat'.format(
rec_dirs[rec_id], rec_fprefix[rec_id], sim_space[space_id],
sim_a[z_id])
Cov_Pk_wnw = np.loadtxt(ifile_Cov_Pk, dtype='f4', comments='#')
ivar_Pk_wnow = N_dataset / np.diag(Cov_Pk_wnw) # the mean sigma error
params_mcmc = mcmc_routine(N_params, N_walkers, N_walkersteps, theta,
params_T, params_indices, fix_params, k_p,
mu_p, Pk_wnw_diff_true, ivar_Pk_wnow,
tck_Pk_linw, tck_Pk_sm, norm_gf,
params_name, pool)
chi_square = chi2(params_mcmc[:, 0], params_indices, fix_params, k_p,
mu_p, Pk_wnw_diff_true, ivar_Pk_wnow, tck_Pk_linw,
tck_Pk_sm, norm_gf)
reduced_chi2 = chi_square / (N_fitbin - N_params)
print('Reduced chi2: {}\n'.format(reduced_chi2))
if rec_id == 1:
if set_Sigma_xyz_theory == "False":
ofile_params = odir + 'sub_{}kave{}.wnw_diff_a_{}_params{}_Sigma_sm{}.dat'.format(
rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id],
''.join(map(str, params_indices)), round(sub_sigma_sm, 3))
else:
ofile_params = odir + 'sub_{}kave{}.wnw_diff_a_{}_params{}_isotropic_Sigmaz_{}_Sigma_sm{}.dat'.format(
rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id],
''.join(map(str, params_indices)), round(Sigma_z, 3),
round(sub_sigma_sm, 3))
elif rec_id == 0:
if set_Sigma_xyz_theory == "False":
ofile_params = odir + 'sub_{}kave{}.wnw_diff_a_{}_params{}.dat'.format(
rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id],
''.join(map(str, params_indices)))
else:
ofile_params = odir + 'sub_{}kave{}.wnw_diff_a_{}_params{}_isotropic_Sigmaz_{}.dat'.format(
rec_fprefix[rec_id], sim_space[space_id], sim_a[z_id],
''.join(map(str, params_indices)), round(Sigma_z, 3))
# write_params(ofile_params, params_mcmc, params_name, reduced_chi2)
pool.close()
try:
# Initialize the MPI-based pool used for parallelization.
pool = MPIPool()
except:
print("Either MPI doesn't seem to be installed or you aren't running with MPI... ")
using_mpi = False
pool=None
if using_mpi:
if not pool.is_master():
# Wait for instructions from the master process.
pool.wait()
sys.exit(0)
else:
print("MPI available for this code! - call this with e.g. mpirun -np 16 python test_betapic_TGAS.py")
sampler = fit_group.fit_one_group(star_params, init_mod=beta_pic_group, \
nwalkers=30, nchain=10000, nburn=1000, return_sampler=True, pool=pool, \
init_sdev = np.array([1,1,1,1,1,1,1,1,1,.01,.01,.01,.1,.1]), background_density=1e-6, use_swig=True, \
plotit=False)
if using_mpi:
# Close the processes.
pool.close()
#print("Autocorrelation lengths: ")
#print(sampler.get_autocorr_time(c=2.5))
pickle.dump((sampler.chain[:,-1,:], sampler.lnprobability[:,-1]), open("betaPic_sampler_end_m06.pkl",'w'))
print("Autocorrelation lengths: ")
print(sampler.get_autocorr_time(c=2.0))
def run_mcmc(cos_twol,sin_twol,sin_l,cos_l,sin_b,cos_b,data_pml,data_err_pml,\
data_pmb,data_err_pmb,data_plx,data_err_plx,data_vlos,data_err_vlos,data_age,\
age_number,distance_number,Number):
distance = distance_list[distance_number]
age = age_list[age_number]
#define the objective function
negativelnLikelihood = lambda *args: -lnlike(*args)[0]
#initial guess for p
p_0 = p0_list[age_number]
#generate random values. np.random.randn provides Gaussian with mean 0 and standard deviation 1
#thus here is adding random values obeying the Gaussian like above to each values.
pos = [p_0 + 1. * np.random.randn(ndim) for i in range(N_WALKERS)]
#for multiprocessing
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
obsevlosables= cos_twol,sin_twol,sin_l,cos_l,sin_b,cos_b,data_pml,data_err_pml,data_pmb,\
data_err_pmb,data_plx,data_err_plx,data_vlos,data_err_vlos,data_age,age_number
sampler = emcee.EnsembleSampler(N_WALKERS,
ndim,
lnprob,
args=obsevlosables)
#sampler = emcee.EnsembleSampler(N_WALKERS, ndim, lnprob, pool=pool, \
# args=(cos_twol,sin_twol,sin_l,cos_l,sin_b,cos_b,data_pml,data_err_pml,data_pmb,\
# data_err_pmb,data_plx,data_err_plx,data_vlos,data_err_vlos))
sampler.run_mcmc(pos, Nrun)
pool.close()
print('Done.')
#---
# store the results
burnin = Nburn
samples = sampler.chain[:, burnin:, :].reshape((-1, ndim))
plt.clf()
hight_fig_inch = np.int((ndim + 1) * 3.0)
fig, axes = plt.subplots(ndim + 1,
1,
sharex=True,
figsize=(8, hight_fig_inch))
for i in range(ndim):
axes[i].plot(sampler.chain[:, :, i].T, color='k', alpha=0.5)
axes[i].set_ylabel(_list_labels[i])
# last panel shows the evolution of ln-likelihood for the ensemble of walkers
axes[-1].plot(sampler.lnprobability.T, color='k', alpha=0.5)
axes[-1].set_ylabel('ln(L)')
maxlnlike = np.max(sampler.lnprobability)
axes[-1].set_ylim(maxlnlike - 3 * ndim, maxlnlike)
fig.tight_layout(h_pad=0.)
filename_pre = 'newModel_1/'+distance+'/line-time_walker%dNrun%dNburn%d_withscatter_'\
+age+'Gyr_'+distance+'_%dstars_newModel_1'
filename = filename_pre % (N_WALKERS, Nrun, Nburn, Number)
fig.savefig(filename + '.png')
# Make a triangle plot
burnin = Nburn
samples = sampler.chain[:, burnin:, :].reshape((-1, ndim))
#convert scatters to exp(scatters)
#samples[:,-3] = np.exp(samples[:,-3])
#samples[:,-2] = np.exp(samples[:,-2])
#samples[:,-1] = np.exp(samples[:,-1])
fig = corner.corner(
samples[:, :-3],
labels=_list_labels,
label_kwargs={'fontsize': 20},
# truths=_list_answer,
quantiles=[0.16, 0.5, 0.84],
plot_datapoints=True,
show_titles=True,
title_args={'fontsize': 20},
title_fmt='.3f',
)
filename_pre = 'newModel_1/'+distance+'/trinagle_walker%dNrun%dNburn%d_withscatter_'\
+age+'Gyr_'+distance+'_%dstars_newModel_1'
filename = filename_pre % (N_WALKERS, Nrun, Nburn, Number)
fig.savefig(filename + '.png')
#fig.savefig(filename+'.pdf')
p = np.mean(samples, axis=0)
e = np.var(samples, axis=0)**0.5
filename = 'newModel_1/result_' + age + 'Gyr_' + distance + '_' + str(
Number) + 'stars_newModel_1' + '.txt'
np.savetxt(filename, (p, e), fmt="%.3f", delimiter=',')
va,vR2,sigmaphi,meanvR,sigmaR =\
lnlike(p,cos_twol,sin_twol,sin_l,cos_l,sin_b,cos_b,data_pml,data_err_pml,data_pmb,\
data_err_pmb,data_plx,data_err_plx,data_vlos,data_err_vlos,data_age,age_number)[1],\
lnlike(p,cos_twol,sin_twol,sin_l,cos_l,sin_b,cos_b,data_pml,data_err_pml,data_pmb,\
data_err_pmb,data_plx,data_err_plx,data_vlos,data_err_vlos,data_age,age_number)[2],\
lnlike(p,cos_twol,sin_twol,sin_l,cos_l,sin_b,cos_b,data_pml,data_err_pml,data_pmb,\
data_err_pmb,data_plx,data_err_plx,data_vlos,data_err_vlos,data_age,age_number)[3],\
lnlike(p,cos_twol,sin_twol,sin_l,cos_l,sin_b,cos_b,data_pml,data_err_pml,data_pmb,\
data_err_pmb,data_plx,data_err_plx,data_vlos,data_err_vlos,data_age,age_number)[4],\
lnlike(p,cos_twol,sin_twol,sin_l,cos_l,sin_b,cos_b,data_pml,data_err_pml,data_pmb,\
data_err_pmb,data_plx,data_err_plx,data_vlos,data_err_vlos,data_age,age_number)[5]
f = open('va_newModel_1.txt', 'a')
printline = '%s, %f, %f, %f, %f, %f, %f\n' % (filename, np.mean(va), vR2,
sigmaphi, np.mean(sigmaR) /
80., meanvR, sigmaR)
f.write(printline)
f.close()
va_list = []
sigmaR = []
print(filename)
return None
def run_emcee_2(M2_d, P_orb_obs, ecc_obs, ra, dec, M2_d_err=1.0,
P_orb_obs_err=1.0, ecc_obs_err=0.05, nwalkers=80, nburn=1000,
nsteps=1000,
threads=1, mpi=False):
""" Run the emcee function
Parameters
----------
M2_d : float
Observed secondary mass
P_orb_obs : float
Observed orbital period
ecc_obs : float
Observed orbital eccentricity
ra : float
Observed right ascension
dec : float
Observed declination
threads : int
Number of threads to use for parallelization
mpi : bool
If true, use MPIPool for parallelization
Returns
-------
sampler : emcee object
"""
# First thing is to load the sse data and SF_history data
load_sse.load_sse()
sf_history.load_sf_history()
# Get initial values
initial_vals = get_initial_values(M2_d, nwalkers=nwalkers)
# Define sampler
args = [[M2_d, M2_d_err, P_orb_obs, P_orb_obs_err, ecc_obs, ecc_obs_err, ra, dec]]
if mpi == True:
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
sampler = emcee.EnsembleSampler(nwalkers=nwalkers, dim=10, lnpostfn=ln_posterior, args=args, pool=pool)
elif threads != 1:
sampler = emcee.EnsembleSampler(nwalkers=nwalkers, dim=10, lnpostfn=ln_posterior, args=args, threads=threads)
else:
sampler = emcee.EnsembleSampler(nwalkers=nwalkers, dim=10, lnpostfn=ln_posterior, args=args)
# Assign initial values
p0 = np.zeros((nwalkers,10))
p0 = set_walkers(initial_vals, args[0], nwalkers=nwalkers)
# Burn-in 1
pos,prob,state = sampler.run_mcmc(p0, N=nburn)
sampler1 = copy.copy(sampler)
# TESTING BEGIN - Get limiting ln_prob for worst 10 chains
prob_lim = (np.sort(prob)[9] + np.sort(prob)[10])/2.0
index_best = np.argmax(prob)
for i in np.arange(len(prob)):
# if sampler1.acceptance_fraction[i] == 0.0: pos[i] = np.copy(pos[index_best]) + np.random.normal(0.0, 0.005, size=10)
if prob[i] < prob_lim: pos[i] = np.copy(pos[index_best]) + np.random.normal(0.0, 0.005, size=10)
# TESTING END
print "Burn-in 1 finished."
print "Starting burn-in 2..."
# Burn-in 2
sampler.reset()
pos,prob,state = sampler.run_mcmc(pos, N=nburn)
sampler2 = copy.copy(sampler)
# TESTING BEGIN - Get limiting ln_prob for worst 10 chains
prob_lim = (np.sort(prob)[9] + np.sort(prob)[10])/2.0
index_best = np.argmax(prob)
for i in np.arange(len(prob)):
# if sampler2.acceptance_fraction[i] == 0.0: pos[i] = np.copy(pos[index_best]) + np.random.normal(0.0, 0.005, size=10)
if prob[i] < prob_lim: pos[i] = np.copy(pos[index_best]) + np.random.normal(0.0, 0.005, size=10)
# TESTING END
print "Burn-in 2 finished."
print "Starting burn-in 3..."
# Burn-in 3
sampler.reset()
pos,prob,state = sampler.run_mcmc(pos, N=nburn)
sampler3 = copy.copy(sampler)
# TESTING BEGIN - Get limiting ln_prob for worst 10 chains
prob_lim = (np.sort(prob)[9] + np.sort(prob)[10])/2.0
index_best = np.argmax(prob)
for i in np.arange(len(prob)):
# if sampler3.acceptance_fraction[i] == 0.0: pos[i] = np.copy(pos[index_best]) + np.random.normal(0.0, 0.005, size=10)
if prob[i] < prob_lim: pos[i] = np.copy(pos[index_best]) + np.random.normal(0.0, 0.005, size=10)
# TESTING END
print "Burn-in 3 finished."
print "Starting burn-in 4..."
# Burn-in 4
sampler.reset()
pos,prob,state = sampler.run_mcmc(pos, N=nburn)
sampler4 = copy.copy(sampler)
print "Burn-in 4 finished."
print "Starting production run..."
# Full run
sampler.reset()
pos,prob,state = sampler.run_mcmc(pos, N=nsteps)
print "Finished production run"
if mpi is True: pool.close()
return sampler1, sampler2, sampler3, sampler4, sampler
def main():
#################################################
############Option parsing#######################
#################################################
#Parse command line options
parser = argparse.ArgumentParser()
parser.add_argument("-f","--file",dest="options_file",action="store",type=str,help="analysis options file")
parser.add_argument("-v","--verbose",dest="verbose",action="store_true",default=False,help="turn on verbosity")
parser.add_argument("-vv","--verbose_plus",dest="verbose_plus",action="store_true",default=False,help="turn on additional verbosity")
parser.add_argument("-m","--mask_scale",dest="mask_scale",action="store_true",default=False,help="scale peaks and power spectrum to unmasked area")
parser.add_argument("-c","--cut_convergence",dest="cut_convergence",action="store",default=None,help="select convergence values in (min,max) to compute the likelihood. Safe for single descriptor only!!")
parser.add_argument("-g","--group_subfields",dest="group_subfields",action="store_true",default=False,help="group feature realizations by taking the mean over subfields, this makes a big difference in the covariance matrix")
parser.add_argument("-s","--save_points",dest="save_points",action="store",default=None,help="save points in parameter space to external npy file")
parser.add_argument("-ss","--save_debug",dest="save_debug",action="store_true",default=False,help="save a bunch of debugging info for the analysis")
parser.add_argument("-p","--prefix",dest="prefix",action="store",default="",help="prefix of the emulator to pickle")
parser.add_argument("-r","--realizations",dest="realizations",type=int,default=None,help="use only the first N realizations to estimate the covariance matrix")
parser.add_argument("-d","--differentiate",dest="differentiate",action="store_true",default=False,help="differentiate the first minkowski functional to get the PDF")
parser.add_argument("-ms","--mean_subtract",dest="mean_subtract",action="store_true",default=False,help="lod in the observations with the subtracted means")
cmd_args = parser.parse_args()
if cmd_args.options_file is None:
parser.print_help()
sys.exit(0)
#Set verbosity level
if cmd_args.verbose_plus:
logging.basicConfig(level=DEBUG_PLUS)
elif cmd_args.verbose:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
#Initialize MPI Pool
try:
pool = MPIPool()
except:
pool = None
if (pool is not None) and (not pool.is_master()):
pool.wait()
sys.exit(0)
if pool is not None:
logging.info("Started MPI Pool.")
#################################################################################################################
#################Info gathering: covariance matrix, observation and emulator#####################################
#################################################################################################################
#start
start = time.time()
last_timestamp = start
#Instantiate a FeatureLoader object that will take care of the memory loading
feature_loader = FeatureLoader(cmd_args)
###########################################################################################################################################
#Use this model for the covariance matrix (from the new set of 50 N body simulations)
covariance_model = CFHTcov.getModels(root_path=feature_loader.options.get("simulations","root_path"))
logging.info("Measuring covariance matrix from model {0}".format(covariance_model))
#Load in the covariance matrix
fiducial_feature_ensemble = feature_loader.load_features(covariance_model)
#If options is enabled, use only the first N realizations to estimate the covariance matrix
if cmd_args.realizations is not None:
logging.info("Using only the first {0} realizations to estimate the covariance matrix".format(cmd_args.realizations))
fiducial_feature_ensemble = fiducial_feature_ensemble.subset(range(cmd_args.realizations))
assert fiducial_feature_ensemble.num_realizations==cmd_args.realizations
fiducial_features = fiducial_feature_ensemble.mean()
features_covariance = fiducial_feature_ensemble.covariance()
#timestamp
now = time.time()
logging.info("covariance loaded in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
################################################################################################################################################
#Get also the observation instance
observation = CFHTLens(root_path=feature_loader.options.get("observations","root_path"))
logging.info("Measuring the observations from {0}".format(observation))
#And load the observations
observed_feature = feature_loader.load_features(observation).mean()
#timestamp
now = time.time()
logging.info("observation loaded in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
################################################################################################################################################
#Create a LikelihoodAnalysis instance by unpickling one of the emulators
emulators_dir = os.path.join(feature_loader.options.get("analysis","save_path"),"emulators")
emulator_file = os.path.join(emulators_dir,"emulator{0}_{1}.p".format(cmd_args.prefix,output_string(feature_loader.feature_string)))
logging.info("Unpickling emulator from {0}...".format(emulator_file))
analysis = LikelihoodAnalysis.load(emulator_file)
#timestamp
now = time.time()
logging.info("emulator unpickled in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
####################################################################################################################
######################################Compute the chi2 cube#########################################################
####################################################################################################################
logging.info("Initializing chi2 meshgrid...")
#Read parameters to use from options
use_parameters = feature_loader.options.get("parameters","use_parameters").replace(" ","").split(",")
assert len(use_parameters)==3
#Reparametrization hash key
use_parameters_hash = "-".join(use_parameters)
########################################################################################
#Might need to reparametrize the emulator here, use a dictionary for reparametrizations#
########################################################################################
assert use_parameters_hash in reparametrization.keys(),"No reparametrization scheme specified for {0} parametrization".format(use_parameters_hash)
if reparametrization[use_parameters_hash] is not None:
#Reparametrize
logging.info("Reparametrizing emulator according to {0} parametrization".format(use_parameters_hash))
analysis.reparametrize(reparametrization[use_parameters_hash])
#Retrain for safety
analysis.train()
#Log current parametrization to user
logging.info("Using parametrization {0}".format(use_parameters_hash))
#Set the points in parameter space on which to compute the chi2 (read extremes from options)
par = list()
for p in range(3):
assert feature_loader.options.has_section(use_parameters[p]),"No extremes specified for parameter {0}".format(use_parameters[p])
par.append(np.ogrid[feature_loader.options.getfloat(use_parameters[p],"min"):feature_loader.options.getfloat(use_parameters[p],"max"):feature_loader.options.getint(use_parameters[p],"num_points")*1j])
num_points = len(par[0]) * len(par[1]) * len(par[2])
points = np.array(np.meshgrid(par[0],par[1],par[2],indexing="ij")).reshape(3,num_points).transpose()
#Now compute the chi2 at each of these points
if pool:
split_chunks = pool.size
logging.info("Computing chi squared for {0} parameter combinations using {1} cores...".format(points.shape[0],pool.size))
else:
split_chunks = None
logging.info("Computing chi squared for {0} parameter combinations using 1 core...".format(points.shape[0]))
chi_squared = analysis.chi2(points,observed_feature=observed_feature,features_covariance=features_covariance,pool=pool,split_chunks=split_chunks)
now = time.time()
logging.info("chi2 calculations completed in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
#Close pool
if pool is not None:
pool.close()
logging.info("Closed MPI Pool.")
#save output
likelihoods_dir = os.path.join(feature_loader.options.get("analysis","save_path"),"likelihoods_{0}".format(use_parameters_hash))
prefix = cmd_args.prefix
if cmd_args.mean_subtract:
prefix += "_meansub"
if not os.path.isdir(likelihoods_dir):
os.mkdir(likelihoods_dir)
if cmd_args.realizations is None:
chi2_file = os.path.join(likelihoods_dir,"chi2{0}_{1}.npy".format(prefix,output_string(feature_loader.feature_string)))
likelihood_file = os.path.join(likelihoods_dir,"likelihood{0}_{1}.npy".format(prefix,output_string(feature_loader.feature_string)))
else:
chi2_file = os.path.join(likelihoods_dir,"chi2{0}{1}real_{2}.npy".format(prefix,cmd_args.realizations,output_string(feature_loader.feature_string)))
likelihood_file = os.path.join(likelihoods_dir,"likelihood{0}{1}real_{2}.npy".format(prefix,cmd_args.realizations,output_string(feature_loader.feature_string)))
logging.info("Saving chi2 to {0}".format(chi2_file))
np.save(chi2_file,chi_squared.reshape(par[0].shape + par[1].shape + par[2].shape))
logging.info("Saving full likelihood to {0}".format(likelihood_file))
likelihood_cube = analysis.likelihood(chi_squared.reshape(par[0].shape + par[1].shape + par[2].shape))
np.save(likelihood_file,likelihood_cube)
#Find the maximum of the likelihood using ContourPlot functionality
contour = ContourPlot()
contour.getLikelihood(likelihood_cube,parameter_axes={use_parameters[0]:0,use_parameters[1]:1,use_parameters[2]:2},parameter_labels={use_parameters[0]:"0",use_parameters[1]:"1",use_parameters[2]:"2"})
contour.getUnitsFromOptions(feature_loader.options)
parameters_maximum = contour.getMaximum()
parameter_keys = parameters_maximum.keys()
parameter_keys.sort(key=contour.parameter_axes.get)
#Display the new best fit before exiting
best_fit_parameters = np.array([ parameters_maximum[par_key] for par_key in parameter_keys ])
logging.info("Best fit is [ {0[0]:.2f} {0[1]:.2f} {0[2]:.2f} ], chi2={1[0]:.3f}({2} dof)".format(best_fit_parameters,analysis.chi2(np.array(best_fit_parameters),features_covariance=features_covariance,observed_feature=observed_feature),analysis.training_set.shape[1]))
#Additionally save some debugging info to plot, etc...
if cmd_args.save_debug:
troubleshoot_dir = os.path.join(feature_loader.options.get("analysis","save_path"),"troubleshoot_{0}".format(use_parameters_hash))
if not os.path.isdir(troubleshoot_dir):
os.mkdir(troubleshoot_dir)
logging.info("Saving troubleshoot info to {0}...".format(troubleshoot_dir))
np.save(os.path.join(troubleshoot_dir,"observation_{0}.npy".format(output_string(feature_loader.feature_string))),observed_feature)
np.save(os.path.join(troubleshoot_dir,"covariance_{0}.npy".format(output_string(feature_loader.feature_string))),features_covariance)
np.save(os.path.join(troubleshoot_dir,"fiducial_{0}.npy".format(output_string(feature_loader.feature_string))),fiducial_features)
np.save(os.path.join(troubleshoot_dir,"best_fit_features_{0}.npy".format(output_string(feature_loader.feature_string))),analysis.predict(best_fit_parameters))
np.save(os.path.join(troubleshoot_dir,"fiducial_from_interpolator_{0}.npy".format(output_string(feature_loader.feature_string))),analysis.predict(np.array([0.26,-1.0,0.800])))
np.save(os.path.join(troubleshoot_dir,"chi2_contributions_{0}.npy".format(output_string(feature_loader.feature_string))),analysis.chi2Contributions(best_fit_parameters,observed_feature=observed_feature,features_covariance=features_covariance))
end = time.time()
logging.info("DONE!!")
logging.info("Completed in {0:.1f}s".format(end-start))
while jj< len(y):
print 'icount, jj',icount,jj
iipix_mask,iipix = WLanalysis.coords2grid(x[jj:jj+istep], y[jj:jj+istep], idata.flatten().reshape(1,-1)[:,jj:jj+istep], size=sizes[Wx-1])
ipix_mask += iipix_mask
ipix += iipix
jj+=istep
print icount,'W%i done coords2grid %s'%(Wx,icount)#,time.strftime("%Y-%m-%d %H:%M")
save(mask_dir+'smaller/weight0_W%i_%i_numpix'%(Wx,icount), ipix)
save(mask_dir+'smaller/weight0_W%i_%i_nummask'%(Wx,icount), ipix_mask)
#ipix is the num. of pixels fall in that big pix, ipix_mask is the mask
return ipix, ipix_mask
p = MPIPool()
if not p.is_master():
p.wait()
sys.exit(0)
#p.map(partialdata2grid, range(63))
ismall_map=p.map(partialdata2grid, range(63))
small_map = sum(array(ismall_map),axis=0)
save(mask_dir+'weight0_W%i_smaller_mask.npy'%(Wx),small_map)
weight=1-small_map[1]/small_map[0]
weight[isnan(weight)]=0
save(mask_dir+'ludoweight_weight0_W%i.npy'%Wx, weight)
mask=weight/weight
mask[isnan(mask)]=0
save(mask_dir+'ludomask_weight0_W%i.npy'%Wx, mask)
p.close()
def main():
#################################################
############Option parsing#######################
#################################################
#Parse command line options
parser = argparse.ArgumentParser()
parser.add_argument("-f","--file",dest="options_file",action="store",type=str,help="analysis options file")
parser.add_argument("-v","--verbose",dest="verbose",action="store_true",default=False,help="turn on verbosity")
parser.add_argument("-vv","--verbose_plus",dest="verbose_plus",action="store_true",default=False,help="turn on additional verbosity")
parser.add_argument("-m","--mask_scale",dest="mask_scale",action="store_true",default=False,help="scale peaks and power spectrum to unmasked area")
parser.add_argument("-c","--cut_convergence",dest="cut_convergence",action="store",default=None,help="select convergence values in (min,max) to compute the likelihood. Safe for single descriptor only!!")
parser.add_argument("-g","--group_subfields",dest="group_subfields",action="store_true",default=False,help="group feature realizations by taking the mean over subfields, this makes a big difference in the covariance matrix")
parser.add_argument("-s","--save_points",dest="save_points",action="store",default=None,help="save points in parameter space to external npy file")
parser.add_argument("-ss","--save_debug",dest="save_debug",action="store_true",default=False,help="save a bunch of debugging info for the analysis")
parser.add_argument("-p","--prefix",dest="prefix",action="store",default="",help="prefix of the emulator to pickle")
parser.add_argument("-r","--remove",dest="remove",action="store",type=int,default=24,help="model to remove from the analysis")
parser.add_argument("-R","--random",dest="random",action="store",type=int,default=0,help="random seed initialization for realization picking")
cmd_args = parser.parse_args()
if cmd_args.options_file is None:
parser.print_help()
sys.exit(0)
#Set verbosity level
if cmd_args.verbose_plus:
logging.basicConfig(level=DEBUG_PLUS)
elif cmd_args.verbose:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
#Initialize MPI Pool
try:
pool = MPIPool()
except:
pool = None
if (pool is not None) and (not pool.is_master()):
pool.wait()
sys.exit(0)
if pool is not None:
logging.info("Started MPI Pool.")
#################################################################################################################
#################Info gathering: covariance matrix, observation and emulator#####################################
#################################################################################################################
#start
start = time.time()
last_timestamp = start
#Instantiate a FeatureLoader object that will take care of the memory loading
feature_loader = FeatureLoader(cmd_args)
###########################################################################################################################################
#Get the names of all the simulated models available for the CFHT analysis, including smoothing scales and subfields
all_simulated_models = CFHTemu1.getModels(root_path=feature_loader.options.get("simulations","root_path"))
#Use this model for the covariance matrix
covariance_model = all_simulated_models[feature_loader.options.getint("analysis","covariance_model")]
logging.info("Measuring covariance matrix from model {0}".format(covariance_model))
#Load in the covariance matrix
features_covariance = feature_loader.load_features(covariance_model).covariance()
#timestamp
now = time.time()
logging.info("covariance loaded in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
################################################################################################################################################
#Create a LikelihoodAnalysis instance by unpickling one of the emulators
emulators_dir = os.path.join(feature_loader.options.get("analysis","save_path"),"emulators")
emulator_file = os.path.join(emulators_dir,"emulator{0}_{1}.p".format(cmd_args.prefix,output_string(feature_loader.feature_string)))
logging.info("Unpickling emulator from {0}...".format(emulator_file))
analysis = LikelihoodAnalysis.load(emulator_file)
#timestamp
now = time.time()
logging.info("emulator unpickled in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
##################################################################################################################################################
#Initialize random seed
np.random.seed(cmd_args.random)
realization = np.random.randint(0,1000)
#Treat the removed model as data
model_to_remove = all_simulated_models[cmd_args.remove]
parameters_to_remove = model_to_remove.squeeze()
logging.info("Treating model {0}, realization {1} as data, loading features...".format(model_to_remove,realization+1))
observed_feature = feature_loader.load_features(model_to_remove)[np.random.randint(0,1000)]
#Compute the chi2 for this observed feature without removing it from the emulator (must be close to 0)
logging.info("Chi2 before removal: {0[0]:.3f} ({1} dof)".format(analysis.chi2(parameters_to_remove,features_covariance=features_covariance,observed_feature=observed_feature),analysis.training_set.shape[1]))
#Remove the model from the emulator
remove_index = analysis.find(parameters_to_remove)[0]
logging.info("Removing model {0} with parameters {1} from emulator...".format(remove_index,analysis.parameter_set[remove_index]))
analysis.remove_model(remove_index)
#Retrain without the removed model
analysis.train()
#Compute the chi2 for this observed feature after removing it from the emulator (likely it's not 0 anymore)
logging.info("Chi2 after removal: {0[0]:.3f} ({1} dof)".format(analysis.chi2(parameters_to_remove,features_covariance=features_covariance,observed_feature=observed_feature),analysis.training_set.shape[1]))
####################################################################################################################
######################################Compute the chi2 cube#########################################################
####################################################################################################################
logging.info("Initializing chi2 meshgrid...")
#Set the points in parameter space on which to compute the chi2 (read from options)
Om = np.ogrid[feature_loader.options.getfloat("Omega_m","min"):feature_loader.options.getfloat("Omega_m","max"):feature_loader.options.getint("Omega_m","num_points")*1j]
w = np.ogrid[feature_loader.options.getfloat("w","min"):feature_loader.options.getfloat("w","max"):feature_loader.options.getint("w","num_points")*1j]
si8 = np.ogrid[feature_loader.options.getfloat("sigma8","min"):feature_loader.options.getfloat("sigma8","max"):feature_loader.options.getint("sigma8","num_points")*1j]
num_points = len(Om) * len(w) * len(si8)
points = np.array(np.meshgrid(Om,w,si8,indexing="ij")).reshape(3,num_points).transpose()
if cmd_args.save_points is not None:
logging.info("Saving points to {0}.npy".format(cmd_args.save_points.rstrip(".npy")))
np.save(cmd_args.save_points.rstrip(".npy")+".npy",points)
#Now compute the chi2 at each of these points
if pool:
split_chunks = pool.size
logging.info("Computing chi squared for {0} parameter combinations using {1} cores...".format(points.shape[0],pool.size))
else:
split_chunks = None
logging.info("Computing chi squared for {0} parameter combinations using 1 core...".format(points.shape[0]))
chi_squared = analysis.chi2(points,observed_feature=observed_feature,features_covariance=features_covariance,pool=pool,split_chunks=split_chunks)
#Close MPI Pool
if pool is not None:
pool.close()
logging.info("Closed MPI Pool.")
now = time.time()
logging.info("chi2 calculations completed in {0:.1f}s".format(now-last_timestamp))
last_timestamp = now
#Save output
likelihood_file = "likelihood_remove{0}_{1}.npy".format(cmd_args.remove,output_string(feature_loader.feature_string))
chi2_file = "chi2_remove{0}_{1}.npy".format(cmd_args.remove,output_string(feature_loader.feature_string))
logging.info("Saving chi2 to {0}".format(chi2_file))
np.save(chi2_file,chi_squared.reshape(Om.shape + w.shape + si8.shape))
logging.info("Saving full likelihood to {0}".format(likelihood_file))
likelihood_cube = analysis.likelihood(chi_squared.reshape(Om.shape + w.shape + si8.shape))
np.save(likelihood_file,likelihood_cube)
#Find the maximum of the likelihood using ContourPlot functionality
contour = ContourPlot()
contour.getLikelihood(likelihood_cube)
contour.getUnitsFromOptions(feature_loader.options)
parameters_maximum = contour.getMaximum()
parameter_keys = parameters_maximum.keys()
parameter_keys.sort(key=contour.parameter_axes.get)
#Display the new best fit before exiting
best_fit_parameters = [ parameters_maximum[par_key] for par_key in parameter_keys ]
logging.info("New best fit is [ {0[0]:.2f} {0[1]:.2f} {0[2]:.2f} ], chi2={1[0]:.3f}".format(best_fit_parameters,analysis.chi2(np.array(best_fit_parameters),features_covariance=features_covariance,observed_feature=observed_feature)))
#End
end = time.time()
logging.info("DONE!!")
logging.info("Completed in {0:.1f}s".format(end-start))
def main(nw=1000,th=9,bi=500,fr=2000,thin=20,runmpi=True,local=False,
dil=None,codedir='/Users/tom/Projects/doug_hz/code',
ldfileloc='/Users/tom/Projects/doug_hz/code/'):
if runmpi:
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
else:
pool=None
#if not local:
#sys.path.append('/u/tsbarcl2/svn_code/tom_code/')
#ldfileloc = '/u/tsbarcl2/svn_code/tom_code/'
#elif local:
#sys.path.append('/Users/tom/svn_code/tom_code/')
#ldfileloc = '/Users/tom/svn_code/tom_code/'
if dil is None:
dil = 0.0
files = os.listdir('.')
dat_d = get_data(files)
rho_prior = True
ldp_prior = False
#mcmc params
nwalkers = nw
threads = th
burnin = bi
fullrun = fr
#use quadratic or 4 parameter limb darkening
n_ldparams = 2
#lc time offset from BJD-24548333.
toffset = (54832.5 + 67.)
#photometric zeropoint
zpt_0 = 1.E-10
#plot?
#doplot=False
################
M = tmod.transitemcee_fitldp(dat_d['nplanets'],dat_d['cadence'],
ldfileloc=ldfileloc)
#M.get_stellar(dat_d['teff'],dat_d['logg'],dat_d['feh'],n_ldparams)
M.get_stellar(dat_d['teff'],
dat_d['logg'],
dat_d['feh'],
n_ldparams,ldp_prior=ldp_prior)
M.already_open(dat_d['time'],
dat_d['flux'],dat_d['err'],
timeoffset=toffset,normalize=False)
rho_vals = np.array([dat_d['rho'],dat_d['rho_unc']])
M.get_rho(rho_vals,rho_prior)
M.get_zpt(zpt_0)
if dil is not None:
M.get_sol(*dat_d['sol_guess'],dil=dil)
else:
M.get_sol(*dat_d['sol_guess'])
M.cut_non_transit(8)
################
stophere = False
if not stophere:
#for threadnum in np.arange(2,32,2):
p0 = M.get_guess(nwalkers)
l_var = np.shape(p0)[1]
N = len([indval for indval in xrange(fullrun)
if indval%thin == 0])
outfile = 'koi{0}_np{1}_prior{2}_dil{3}.hdf5'.format(
dat_d['koi'],dat_d['nplanets'],rho_prior,dil)
with h5py.File(outfile, u"w") as f:
f.create_dataset("time", data=M.time)
f.create_dataset("flux", data=M.flux)
f.create_dataset("err", data=M.err)
f.create_dataset("itime", data=M._itime)
f.create_dataset("ntt", data = M._ntt)
f.create_dataset("tobs", data = M._tobs)
f.create_dataset("omc",data = M._omc)
f.create_dataset("datatype",data = M._datatype)
f.attrs["rho_0"] = M.rho_0
f.attrs["rho_0_unc"] = M.rho_0_unc
f.attrs["nplanets"] = M.nplanets
f.attrs["ld1"] = M.ld1
f.attrs["ld2"] = M.ld2
f.attrs["koi"] = dat_d['koi']
f.attrs["dil"] = dil
g = f.create_group("mcmc")
g.attrs["nwalkers"] = nwalkers
g.attrs["burnin"] = burnin
g.attrs["iterations"] = fullrun
g.attrs["thin"] = thin
g.attrs["rho_prior"] = rho_prior
g.attrs["ldp_prior"] = ldp_prior
g.attrs["onlytransits"] = M.onlytransits
g.attrs["tregion"] = M.tregion
g.attrs["ldfileloc"] = M.ldfileloc
g.attrs["n_ldparams"] = M.n_ldparams
g.create_dataset("fixed_sol", data= M.fixed_sol)
g.create_dataset("fit_sol_0", data= M.fit_sol_0)
c_ds = g.create_dataset("chain",
(nwalkers, N, l_var),
dtype=np.float64)
lp_ds = g.create_dataset("lnprob",
(nwalkers, N),
dtype=np.float64)
#args = [M.nplanets,M.rho_0,M.rho_0_unc,M.rho_prior,
# M.Teff,M.Teff_unc,M.logg,M.logg_unc,M.FeH,M.FeH_unc,
# M.flux,M.err,M.fixed_sol,M.time,M._itime,M._ntt,
# M._tobs,M._omc,M._datatype,M.n_ldparams,M.ldfileloc,
# M.onlytransits,M.tregion]
args = [M.nplanets,M.rho_0,M.rho_0_unc,M.rho_prior,
M.ld1,M.ld1_unc,M.ld2,M.ld2_unc,M.ldp_prior,
M.flux,M.err,M.fixed_sol,M.time,M._itime,M._ntt,
M._tobs,M._omc,M._datatype,M.n_ldparams,M.ldfileloc,
M.onlytransits,M.tregion]
tom = tmod.logchi2_fitldp
if runmpi:
sampler = emcee.EnsembleSampler(nwalkers, l_var, tom,
args=args,pool=pool)
else:
sampler = emcee.EnsembleSampler(nwalkers, l_var, tom,
args=args,threads=th)
time1 = thetime.time()
p2, prob, state = sampler.run_mcmc(p0, burnin,
storechain=False)
sampler.reset()
with h5py.File(outfile, u"a") as f:
g = f["mcmc"]
g.create_dataset("burnin_pos", data=p2)
g.create_dataset("burnin_prob", data=prob)
time2 = thetime.time()
print 'burn-in took ' + str((time2 - time1)/60.) + ' min'
time1 = thetime.time()
for i, (pos, lnprob, state) in enumerate(sampler.sample(p2,
iterations=fullrun, rstate0=state,
storechain=False)):
#do the thinning in the loop here
if i % thin == 0:
ind = i / thin
with h5py.File(outfile, u"a") as f:
g = f["mcmc"]
c_ds = g["chain"]
lp_ds = g["lnprob"]
c_ds[:, ind, :] = pos
lp_ds[:, ind] = lnprob
time2 = thetime.time()
print 'MCMC run took ' + str((time2 - time1)/60.) + ' min'
print
print("Mean acceptance: "
+ str(np.mean(sampler.acceptance_fraction)))
print
#try:
# print("Autocorrelation time:", sampler.acor)
# print("Autocorrelation times sampled:",
# fullrun / sampler.acor)
#except RuntimeError:
# print("No Autocorrelation")
if runmpi:
pool.close()
# if doplot:
# plt.ioff()
# import triangle
# labels=[r"rho", r"zpt"]
# for ij in xrange(dat_d['nplanets']):
# labels = np.r_[labels,[r"T0",
# r"per",r"b", r"rprs", r"ecosw",r"esinw"]]
# figure = triangle.corner(sampler.flatchain, labels=labels)
# figure.savefig("data.png")
#savefile = 'koi%s_np%s_prior%s.dat' %(dat_d['koi'],
# dat_d['nplanets'],rho_prior)
#savefile2 = 'koi%s_np%s_prior%s_prob.dat' %(dat_d['koi'],
# dat_d['nplanets'],rho_prior)
#np.savetxt(savefile,sampler.flatchain)
#np.savetxt(savefile2,sampler.flatlnprobability)
return sampler
def LensModelMCMC(data,lens,source,
xmax=30.,highresbox=[-3.,3.,-3.,3.],emitres=None,fieldres=None,
sourcedatamap=None, scaleamp=False, shiftphase=False,
modelcal=True,cosmo=Planck15,
nwalkers=1e3,nburn=1e3,nstep=1e3,pool=None,nthreads=1,mpirun=False):
"""
Wrapper function which basically takes what the user wants and turns it into the
format needed for the acutal MCMC lens modeling.
Inputs:
data:
One or more visdata objects; if multiple datasets are being
fit to, should be a list of visdata objects.
lens:
Any of the currently implemented lens objects or ExternalShear.
source:
One or more of the currently implemented source objects; if more than
one source to be fit, should be a list of multiple sources.
xmax:
(Half-)Grid size, in arcseconds; the grid will span +/-xmax in x&y
highresbox:
The region to model at higher resolution (to account for high-magnification
and differential lensing effects), as [xmin, xmax, ymin, ymax].
Note the sign convention is: +x = West, +y = North, like the lens
positions.
sourcedatamap:
A list of length the number of datasets which tells which source(s)
are to be fit to which dataset(s). Eg, if two sources are to be fit
to two datasets jointly, should be [[0,1],[0,1]]. If we have four
sources and three datasets, could be [[0,1],[0,1],[2,3]] to say that the
first two sources should both be fit to the first two datasets, while the
second two should be fit to the third dataset. If None, will assume
all sources should be fit to all datasets.
scaleamp:
A list of length the number of datasets which tells whether a flux
rescaling is allowed and which dataset the scaling should be relative to.
False indicates no scaling should be done, while True indicates that
amplitude scaling should be allowed.
shiftphase:
Similar to scaleamp above, but allowing for positional/astrometric offsets.
modelcal:
Whether or not to perform the pseudo-selfcal procedure of H+13
cosmo:
The cosmology to use, as an astropy object, e.g.,
from astropy.cosmology import WMAP9; cosmo=WMAP9
Default is Planck15.
nwalkers:
Number of walkers to use in the mcmc process; see dan.iel.fm/emcee/current
for more details.
nburn:
Number of burn-in steps to take with the chain.
nstep:
Number of actual steps to take in the mcmc chains after the burn-in
nthreads:
Number of threads (read: cores) to use during the fitting, default 1.
mpirun:
Whether to parallelize using MPI instead of multiprocessing. If True,
nthreads has no effect, and your script should be run with, eg,
mpirun -np 16 python lensmodel.py.
Returns:
mcmcresult:
A nested dict containing the chains requested. Will have all the MCMC
chain results, plus metadata about the run (initial params, data used,
etc.). Formatting still a work in progress (esp. for modelcal phases).
chains:
The raw chain data, for testing.
blobs:
Everything else returned by the likelihood function; will have
magnifications and any modelcal phase offsets at each step; eventually
will remove this once get everything packaged up for mcmcresult nicely.
colnames:
Basically all the keys to the mcmcresult dict; eventually won't need
to return this once mcmcresult is packaged up nicely.
"""
if pool: nthreads = 1
elif mpirun:
nthreads = 1
from emcee.utils import MPIPool
pool = MPIPool(debug=False,loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
else: pool = None
# Making these lists just makes later stuff easier since we now know the dtype
lens = list(np.array([lens]).flatten())
source = list(np.array([source]).flatten()) # Ensure source(s) are a list
data = list(np.array([data]).flatten()) # Same for dataset(s)
scaleamp = list(np.array([scaleamp]).flatten())
shiftphase = list(np.array([shiftphase]).flatten())
modelcal = list(np.array([modelcal]).flatten())
if len(scaleamp)==1 and len(scaleamp)<len(data): scaleamp *= len(data)
if len(shiftphase)==1 and len(shiftphase)<len(data): shiftphase *= len(data)
if len(modelcal)==1 and len(modelcal)<len(data): modelcal *= len(data)
if sourcedatamap is None: sourcedatamap = [None]*len(data)
# emcee isn't very flexible in terms of how it gets initialized; start by
# assembling the user-provided info into a form it likes
ndim, p0, colnames = 0, [], []
# Lens(es) first
for i,ilens in enumerate(lens):
if ilens.__class__.__name__=='SIELens':
for key in ['x','y','M','e','PA']:
if not vars(ilens)[key]['fixed']:
ndim += 1
p0.append(vars(ilens)[key]['value'])
colnames.append(key+'L'+str(i))
elif ilens.__class__.__name__=='ExternalShear':
for key in ['shear','shearangle']:
if not vars(ilens)[key]['fixed']:
ndim += 1
p0.append(vars(ilens)[key]['value'])
colnames.append(key)
# Then source(s)
for i,src in enumerate(source):
if src.__class__.__name__=='GaussSource':
for key in ['xoff','yoff','flux','width']:
if not vars(src)[key]['fixed']:
ndim += 1
p0.append(vars(src)[key]['value'])
colnames.append(key+'S'+str(i))
elif src.__class__.__name__=='SersicSource':
for key in ['xoff','yoff','flux','majax','index','axisratio','PA']:
if not vars(src)[key]['fixed']:
ndim += 1
p0.append(vars(src)[key]['value'])
colnames.append(key+'S'+str(i))
elif src.__class__.__name__=='PointSource':
for key in ['xoff','yoff','flux']:
if not vars(src)[key]['fixed']:
ndim += 1
p0.append(vars(src)[key]['value'])
colnames.append(key+'S'+str(i))
# Then flux rescaling; only matters if >1 dataset
for i,t in enumerate(scaleamp[1:]):
if t:
ndim += 1
p0.append(1.) # Assume 1.0 scale factor to start
colnames.append('ampscale_dset'+str(i+1))
# Then phase/astrometric shift; each has two vals for a shift in x&y
for i,t in enumerate(shiftphase[1:]):
if t:
ndim += 2
p0.append(0.); p0.append(0.) # Assume zero initial offset
colnames.append('astromshift_x_dset'+str(i+1))
colnames.append('astromshift_y_dset'+str(i+1))
# Get any model-cal parameters set up. The process involves some expensive
# matrix inversions, but these only need to be done once, so we'll do them
# now and pass the results as arguments to the likelihood function. See docs
# in calc_likelihood.model_cal for more info.
for i,dset in enumerate(data):
if modelcal[i]:
uniqant = np.unique(np.asarray([dset.ant1,dset.ant2]).flatten())
dPhi_dphi = np.zeros((uniqant.size-1,dset.u.size))
for j in range(1,uniqant.size):
dPhi_dphi[j-1,:]=(dset.ant1==uniqant[j])-1*(dset.ant2==uniqant[j])
C = scipy.sparse.diags((dset.sigma/dset.amp)**-2.,0)
F = np.dot(dPhi_dphi,C*dPhi_dphi.T)
Finv = np.linalg.inv(F)
FdPC = np.dot(-Finv,dPhi_dphi*C)
modelcal[i] = [dPhi_dphi,FdPC]
# Create our lensing grid coordinates now, since those shouldn't be
# recalculated with every call to the likelihood function
xmap,ymap,xemit,yemit,indices = GenerateLensingGrid(data,xmax,highresbox,
fieldres,emitres)
# Calculate the uv coordinates we'll interpolate onto; only need to calculate
# this once, so do it here.
kmax = 0.5/((xmap[0,1]-xmap[0,0])*arcsec2rad)
ug = np.linspace(-kmax,kmax,xmap.shape[0])
# Calculate some distances; we only need to calculate these once.
# This assumes multiple sources are all at same z; should be this
# way anyway or else we'd have to deal with multiple lensing planes
if cosmo is None: cosmo = Planck15
Dd = cosmo.angular_diameter_distance(lens[0].z).value
Ds = cosmo.angular_diameter_distance(source[0].z).value
Dds= cosmo.angular_diameter_distance_z1z2(lens[0].z,source[0].z).value
p0 = np.array(p0)
# Create a ball of starting points for the walkers, gaussian ball of
# 10% width; if initial value is 0 (eg, astrometric shift), give a small sigma
# for angles, generally need more spread than 10% to sample well, do 30% for those cases [~0.5% >180deg for p0=100deg]
isangle = np.array([0.30 if 'PA' in s or 'angle' in s else 0.1 for s in colnames])
initials = emcee.utils.sample_ball(p0,np.asarray([isangle[i]*x if x else 0.05 for i,x in enumerate(p0)]),int(nwalkers))
# All the lens objects know if their parameters have been altered since the last time
# we calculated the deflections. If all the lens pars are fixed, we only need to do the
# deflections once. This step ensures that the lens object we create the sampler with
# has these initial deflections.
for i,ilens in enumerate(lens):
if ilens.__class__.__name__ == 'SIELens': ilens.deflect(xemit,yemit,Dd,Ds,Dds)
elif ilens.__class__.__name__ == 'ExternalShear': ilens.deflect(xemit,yemit,lens[0])
# Create the sampler object; uses calc_likelihood function defined elsewhere
lenssampler = emcee.EnsembleSampler(nwalkers,ndim,calc_vis_lnlike,
args = [data,lens,source,Dd,Ds,Dds,ug,
xmap,ymap,xemit,yemit,indices,
sourcedatamap,scaleamp,shiftphase,modelcal],
threads=nthreads,pool=pool)
# Run burn-in phase
print("Running burn-in... ")
#pos,prob,rstate,mus = lenssampler.run_mcmc(initials,nburn,storechain=False)
for i,result in enumerate(lenssampler.sample(initials,iterations=nburn,storechain=False)):
if i%20==0: print('Burn-in step ',i,'/',nburn)
pos,prob,rstate,blob = result
lenssampler.reset()
# Run actual chains
print("Done. Running chains... ")
for i,result in enumerate(lenssampler.sample(pos,rstate0=rstate,iterations=nstep,storechain=True)):
if i%20==0: print('Chain step ',i,'/',nstep)
#lenssampler.run_mcmc(pos,nstep,rstate0=rstate)
if mpirun: pool.close()
print("Mean acceptance fraction: ",np.mean(lenssampler.acceptance_fraction))
#return lenssampler.flatchain,lenssampler.blobs,colnames
# Package up the magnifications and modelcal phases; disregards nan points (where
# we failed the prior, usu. because a periodic angle wrapped).
blobs = lenssampler.blobs
mus = np.asarray([[a[0] for a in l] for l in blobs]).flatten(order='F')
bad = np.where(np.asarray([np.any(np.isnan(m)) for m in mus],dtype=bool))[0]
for k in bad: mus[k] = np.array([np.nan]*len(source))
mus = np.asarray(list(mus),dtype=float).reshape((-1,len(source)),order='F') # stupid-ass hack
bad = np.isnan(mus)[:,0]
#bad = bad.reshape((-1,len(source)),order='F')[:,0]
#mus = np.atleast_2d(np.asarray([mus[i] if not bad[i] else [np.nan]*len(source) for i in range(mus.size)])).T
colnames.extend(['mu{0:.0f}'.format(i) for i in range(len(source))])
# Assemble the output. Want to return something that contains both the MCMC chains
# themselves, but also metadata about the run.
mcmcresult = {}
# keep track of git revision, for reproducibility's sake
# if run under mpi, this will spew some scaremongering warning text,
# but it's fine. use --mca mpi_warn_on_fork 0 in the mpirun statement to disable
try:
import subprocess
gitd = os.path.abspath(os.path.join(os.path.dirname(__file__),os.pardir))
mcmcresult['githash'] = subprocess.check_output('git --git-dir={0:s} --work-tree={1:s} '\
'rev-parse HEAD'.format(gitd+'/.git',gitd),shell=True).rstrip()
except:
mcmcresult['githash'] = 'No repo found'
mcmcresult['datasets'] = [dset.filename for dset in data] # Data files used
mcmcresult['lens_p0'] = lens # Initial params for lens,src(s),shear; also tells if fixed, priors, etc.
mcmcresult['source_p0'] = source
if sourcedatamap: mcmcresult['sourcedatamap'] = sourcedatamap
mcmcresult['xmax'] = xmax
mcmcresult['highresbox'] = highresbox
mcmcresult['fieldres'] = fieldres
mcmcresult['emitres'] = emitres
if any(scaleamp): mcmcresult['scaleamp'] = scaleamp
if any(shiftphase): mcmcresult['shiftphase'] = shiftphase
mcmcresult['chains'] = np.core.records.fromarrays(np.hstack((lenssampler.flatchain[~bad],mus[~bad])).T,names=colnames)
mcmcresult['lnlike'] = lenssampler.flatlnprobability[~bad]
# Keep track of best-fit params, derived from chains.
c = copy.deepcopy(mcmcresult['chains'])
mcmcresult['best-fit'] = {}
pbest = []
# Calculate the best fit values as medians of each param
lens,source = copy.deepcopy(mcmcresult['lens_p0']), copy.deepcopy(mcmcresult['source_p0'])
for i,ilens in enumerate(lens):
if ilens.__class__.__name__ == 'SIELens':
ilens.__dict__['_altered'] = True
for key in ['x','y','M','e','PA']:
if not vars(ilens)[key]['fixed']:
ilens.__dict__[key]['value'] = np.median(c[key+'L'+str(i)])
pbest.append(np.median(c[key+'L'+str(i)]))
elif ilens.__class__.__name__ == 'ExternalShear':
for key in ['shear','shearangle']:
if not vars(ilens)[key]['fixed']:
ilens.__dict__[key]['value'] = np.median(c[key])
pbest.append(np.median(c[key]))
mcmcresult['best-fit']['lens'] = lens
# now do the source(s)
for i,src in enumerate(source): # Source is a list of source objects
if src.__class__.__name__ == 'GaussSource':
for key in ['xoff','yoff','flux','width']:
if not vars(src)[key]['fixed']:
src.__dict__[key]['value'] = np.median(c[key+'S'+str(i)])
pbest.append(np.median(c[key+'S'+str(i)]))
elif src.__class__.__name__ == 'SersicSource':
for key in ['xoff','yoff','flux','majax','index','axisratio','PA']:
if not vars(src)[key]['fixed']:
src.__dict__[key]['value'] = np.median(c[key+'S'+str(i)])
pbest.append(np.median(c[key+'S'+str(i)]))
elif src.__class__.__name__ == 'PointSource':
for key in ['xoff','yoff','flux']:
if not vars(src)[key]['fixed']:
src.__dict__[key]['value'] = np.median(c[key+'S'+str(i)])
pbest.append(np.median(c[key+'S'+str(i)]))
mcmcresult['best-fit']['source'] = source
mcmcresult['best-fit']['magnification'] = np.median(mus[~bad],axis=0)
# Any amplitude scaling or astrometric shifts
bfscaleamp = np.ones(len(data))
if 'scaleamp' in mcmcresult.keys():
for i,t in enumerate(mcmcresult['scaleamp']): # only matters if >1 datasets
if i==0: pass
elif t:
bfscaleamp[i] = np.median(c['ampscale_dset'+str(i)])
pbest.append(np.median(c['ampscale_dset'+str(i)]))
else: pass
mcmcresult['best-fit']['scaleamp'] = bfscaleamp
bfshiftphase = np.zeros((len(data),2))
if 'shiftphase' in mcmcresult.keys():
for i,t in enumerate(mcmcresult['shiftphase']):
if i==0: pass # only matters if >1 datasets
elif t:
bfshiftphase[i][0] = np.median(c['astromshift_x_dset'+str(i)])
bfshiftphase[i][1] = np.median(c['astromshift_y_dset'+str(i)])
pbest.append(np.median(c['astromshift_x_dset'+str(i)]))
pbest.append(np.median(c['astromshift_y_dset'+str(i)]))
else: pass # no shifting
mcmcresult['best-fit']['shiftphase'] = bfshiftphase
mcmcresult['best-fit']['lnlike'] = calc_vis_lnlike(pbest,data,mcmcresult['best-fit']['lens'],
mcmcresult['best-fit']['source'],
Dd,Ds,Dds,ug,xmap,ymap,xemit,yemit,indices,
sourcedatamap,scaleamp,shiftphase,modelcal)[0]
# Calculate the deviance information criterion, using the Spiegelhalter+02 definition (cf Gelman+04)
mcmcresult['best-fit']['DIC'] = -4*np.mean(mcmcresult['lnlike']) + 2*mcmcresult['best-fit']['lnlike']
# If we did any modelcal stuff, keep the antenna phase offsets here
if any(modelcal):
mcmcresult['modelcal'] = [True if j else False for j in modelcal]
dp = np.squeeze(np.asarray([[a[1] for a in l if ~np.any(np.isnan(a[0]))] for l in blobs]))
a = [x for l in dp for x in l] # Have to dick around with this if we had any nan's
dphases = np.squeeze(np.reshape(a,(nwalkers*nstep-bad.sum(),len(data),-1),order='F'))
if len(data) > 1:
for i in range(len(data)):
if modelcal[i]: mcmcresult['calphases_dset'+str(i)] = np.vstack(dphases[:,i])
else:
if any(modelcal): mcmcresult['calphases_dset0'] = dphases
return mcmcresult
def main(runmpi=True,nw=100,th=6,bi=10,fr=10):
if runmpi:
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
else:
pool=None
#ldfileloc = '/Users/tom/Projects/koi2133/code/'
ldfileloc = '/nobackup/tsbarcl2/Projects/koi2133/code/'
#codedir = '/Users/tom/Projects/koi2133/code'
codedir = '/nobackup/tsbarcl2/Projects/koi2133/code'
koi = 2133
cadence=1625.3
teff = 4550.
teff_unc = 75.
feh = 0.11
feh_unc = 0.07
logg = 2.943
logg_unc = 0.007
rho = 0.0073
rho_unc = 0.0001
nplanets = 1
dil=0.0
period=6.24672336
impact=0.7
T0=136.383880
rprs=0.02067
alb=30.
occ=40.
ell=30.
rvamp=79.0
ecosw=0.048
esinw=-0.045
planet_guess = np.array([
T0,period,impact,rprs,ecosw,esinw,
rvamp,occ,ell,alb])
rvtime, rvval, rverr = get_rv()
time,flux,ferr = get_lc()
rho_prior = True
ldp_prior = False
nwalkers = nw
threads = th
burnin = bi
fullrun = fr
thin = 1
n_ldparams = 2
toffset_lc = 0
toffset_rv = 0
zpt_0 = 1.E-10
M = tmod.transitemcee_koi2133(
nplanets,cadence,
ldfileloc=ldfileloc,codedir=codedir)
M.get_stellar(teff,
logg,
feh,
n_ldparams,ldp_prior=ldp_prior)
M.already_open(time,
flux,ferr,
rvtime,rvval,
rverr,
timeoffset=toffset_lc,rvtimeoffset=toffset_rv,
normalize=False)
rho_vals = np.array([rho,rho_unc])
M.get_rho(rho_vals,rho_prior)
M.get_zpt(zpt_0)
noise_model = [3.0E-4, 3.7E-2, 2.E-4, 3.]
if dil is not None:
M.get_sol(*planet_guess,dil=dil,noise_model=noise_model)
else:
M.get_sol(*planet_guess,noise_model=noise_model)
outfile = 'koi{0}_np{1}_prior{2}_dil{3}GP.hdf5'.format(
koi,nplanets,rho_prior,dil)
p0 = M.get_guess(nwalkers)
#dirty hack!!
qwe = np.r_[np.arange(0,7),np.arange(9,21)]
p0 = p0[:,qwe]
l_var = np.shape(p0)[1]
N = len([indval for indval in xrange(fullrun)
if indval%thin == 0])
with h5py.File(outfile, u"w") as f:
f.create_dataset("time", data=M.time)
f.create_dataset("flux", data=M.flux)
f.create_dataset("err", data=M.err)
f.create_dataset("rvtime", data=M.rvtime)
f.create_dataset("rvval", data=M.rvval)
f.create_dataset("rverr", data=M.rverr)
f.create_dataset("itime", data=M._itime)
f.create_dataset("ntt", data = M._ntt)
f.create_dataset("tobs", data = M._tobs)
f.create_dataset("omc",data = M._omc)
f.create_dataset("datatype",data = M._datatype)
f.attrs["rho_0"] = M.rho_0
f.attrs["rho_0_unc"] = M.rho_0_unc
f.attrs["nplanets"] = M.nplanets
f.attrs["ld1"] = M.ld1
f.attrs["ld2"] = M.ld2
f.attrs["koi"] = koi
f.attrs["dil"] = dil
g = f.create_group("mcmc")
g.attrs["nwalkers"] = nwalkers
g.attrs["burnin"] = burnin
g.attrs["iterations"] = fullrun
g.attrs["thin"] = thin
g.attrs["rho_prior"] = rho_prior
g.attrs["ldp_prior"] = ldp_prior
g.attrs["onlytransits"] = M.onlytransits
g.attrs["tregion"] = M.tregion
g.attrs["ldfileloc"] = M.ldfileloc
g.attrs["n_ldparams"] = M.n_ldparams
g.create_dataset("fixed_sol", data= M.fixed_sol)
g.create_dataset("fit_sol_0", data= M.fit_sol_0)
c_ds = g.create_dataset("chain",
(nwalkers, N, l_var),
dtype=np.float64)
lp_ds = g.create_dataset("lnprob",
(nwalkers, N),
dtype=np.float64)
#I don't like the default LDP unc
#I'm changing them
M.ld1_unc = 0.8
M.ld2_unc = 0.8
args = [M.nplanets,M.rho_0,M.rho_0_unc,M.rho_prior,
M.ld1,M.ld1_unc,M.ld2,M.ld2_unc,M.ldp_prior,
M.flux,M.err,M.fixed_sol,M.time,M._itime,M._ntt,
M._tobs,M._omc,M._datatype,
M.rvtime,M.rvval,M.rverr,M._rvitime,
M.n_ldparams,M.ldfileloc,
M.onlytransits,M.tregion]
tom = tmod.logchi2_rv_phaseGP2
if runmpi:
sampler = emcee.EnsembleSampler(nwalkers, l_var, tom,
args=args,pool=pool)
else:
sampler = emcee.EnsembleSampler(nwalkers, l_var, tom,
args=args,threads=th)
time1 = thetime.time()
p2, prob, state = sampler.run_mcmc(p0, burnin,
storechain=False)
sampler.reset()
with h5py.File(outfile, u"a") as f:
g = f["mcmc"]
g.create_dataset("burnin_pos", data=p2)
g.create_dataset("burnin_prob", data=prob)
time2 = thetime.time()
print('burn-in took ' + str((time2 - time1)/60.) + ' min')
time1 = thetime.time()
for i, (pos, lnprob, state) in enumerate(sampler.sample(p2,
iterations=fullrun, rstate0=state,
storechain=False)):
#do the thinning in the loop here
if i % thin == 0:
ind = i / thin
with h5py.File(outfile, u"a") as f:
g = f["mcmc"]
c_ds = g["chain"]
lp_ds = g["lnprob"]
c_ds[:, ind, :] = pos
lp_ds[:, ind] = lnprob
time2 = thetime.time()
print('MCMC run took ' + str((time2 - time1)/60.) + ' min')
print('')
print("Mean acceptance: "
+ str(np.mean(sampler.acceptance_fraction)))
print('')
if runmpi:
pool.close()
else:
sampler.pool.close()
return sampler
def mcmc(zmin , zmax , iteration):
ndim, nwalkers = 16, 50
bounds = [(-0.2, 0.2), (-0.2, 0.2),(-0.2,0.2),\
(1.5, 3.0) , (0.7, 2.0) , (0.3, 1.0),\
(-20.0,-1.0),(-20.0,-2.0),(-20.0,-2.0),\
(0, 1),(0.0, 4.0), (0,2.0), (0,1),\
(-7.2, 10.0),(-7.2, 10.0),(-7.2, 10.0)]
p0 = np.array([0.0, 0.0, 0.0, 2.0, 1.0, 0.5 , np.log(0.1), np.log(0.1),np.log(0.1),
0.7,1.5,1.0,0.4,np.log(2.0),np.log(2.0),np.log(2.0)])
p0 = [p0 + 1e-5 * np.random.randn(ndim) for k in range(nwalkers)]
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
# Set up the sampler.
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob , pool=pool)
#sampler.sample(p0, 1000)
#print sampler.chain.shape
it = 0
for result in sampler.sample(p0, iterations = 1000):
print it
it += 1
# Run a burn-in chain and save the final location.
#pos, _, _, _ = sampler.run_mcmc(p0, 3000)
#pos, _, _, _ = sampler.sample(p0, 3000)
from matplotlib.ticker import MaxNLocator
sample = sampler.chain
npars = sample.shape[2]
fig , axes = plt.subplots(npars , 1 , sharex=True, figsize=(10, 12))
for i in xrange(npars):
axes[i].plot(sample[:, :, i].T, color="b", alpha=.4 , lw = .5)
axes[i].yaxis.set_major_locator(MaxNLocator(5))
axes[i].set_ylim([bounds[i][0], bounds[i][1]])
axes[i].set_xlim(0, 5000)
#axes[i].set_ylabel(labels[i], fontsize=25)
axes[-1].set_xlabel("Step Number", fontsize=25)
fig.tight_layout(h_pad=0.0)
fig_file = "/home/vakili/public_html/files/redsequence_all_temp/"+str(zmin)+"_z_"+str(zmax)+"burn_iter"+str(iteration)+".png"
plt.savefig(fig_file)
plt.close()
# Run the production chain.
#sampler.reset()
#sampler.run_mcmc(pos, 1000)
"""
import corner
labels = ["$m$", "$b$", "\ln f", "$Q$", "$M$", "$\ln V$"]
#truths = true_params + [true_frac, true_outliers[0], np.log(true_outliers[1])]
bounds = [(-0.2, 0.2), (0.7,2.0), (-20.0, -2.0), (0, 1), (0.0, 2.0), (-7.2, 5.2)]
#corner.corner(sampler.flatchain, bins=35, range=bounds, labels=labels)
#plt.savefig("/home/vakili/public_html/files/mcmc.png")
#plt.close()
"""
sample = sampler.chain
pool.close()
npars = sample.shape[2]
fig , axes = plt.subplots(npars , 1 , sharex=True, figsize=(10, 12))
for i in xrange(npars):
axes[i].plot(sample[:, :, i].T, color="b", alpha=.4 , lw = .5)
axes[i].yaxis.set_major_locator(MaxNLocator(5))
axes[i].set_ylim([bounds[i][0], bounds[i][1]])
axes[i].set_xlim(0, 1500)
#axes[i].set_ylabel(labels[i], fontsize=25)
axes[-1].set_xlabel("Step Number", fontsize=25)
fig.tight_layout(h_pad=0.0)
fig_file = "/home/vakili/public_html/files/redsequence_all_temp/"+str(zmin)+"_z_"+str(zmax)+"chain_iter"+str(iteration)+".png"
plt.savefig(fig_file)
plt.close()
"""
est = np.median(sampler.flatchain , axis = 0)
est[2] = np.median(np.exp(sampler.flatchain)**.5 , axis = 0)[2]
est_err = np.std(sampler.flatchain , axis = 0)
est_err[2] = np.std(np.exp(sampler.flatchain)**.5 , axis = 0)[2]
xx = np.linspace(14.5 , 25.5 , 1000)
pred = est[1] + est[0]*(xx - 19)
"""
return None
"""
norm = 0.0
post_prob = np.zeros(len(x))
for i in range(sampler.chain.shape[1]):
for j in range(sampler.chain.shape[0]):
ll_fg, ll_bg = sampler.blobs[i][j]
post_prob += np.exp(ll_fg - np.logaddexp(ll_fg, ll_bg))
norm += 1
post_prob /= norm
print post_prob
"""
"""
def main(argv):
##################
#These change a lot
numWaveforms = 16
numThreads = 12
ndim = 6 * numWaveforms + 8
nwalkers = 2 * ndim
iter = 50
burnIn = 40
wfPlotNumber = 10
######################
# plt.ion()
fitSamples = 200
#Prepare detector
zero_1 = -5.56351644e+07
pole_1 = -1.38796386e+04
pole_real = -2.02559385e+07
pole_imag = 9885315.37450211
zeros = [zero_1, 0]
poles = [pole_real + pole_imag * 1j, pole_real - pole_imag * 1j, pole_1]
system = signal.lti(zeros, poles, 1E7)
tempGuess = 77.89
gradGuess = 0.0483
pcRadGuess = 2.591182
pcLenGuess = 1.613357
#Create a detector model
detName = "conf/P42574A_grad%0.2f_pcrad%0.2f_pclen%0.2f.conf" % (0.05, 2.5,
1.65)
det = Detector(detName,
temperature=tempGuess,
timeStep=1.,
numSteps=fitSamples * 10,
tfSystem=system)
det.LoadFields("P42574A_fields_v3.npz")
det.SetFields(pcRadGuess, pcLenGuess, gradGuess)
tempIdx = -8
gradIdx = -7
pcRadIdx = -6
pcLenIdx = -5
#and the remaining 4 are for the transfer function
fig_size = (20, 10)
#Create a decent start guess by fitting waveform-by-waveform
wfFileName = "P42574A_512waveforms_%drisetimeculled.npz" % numWaveforms
if os.path.isfile(wfFileName):
data = np.load(wfFileName)
results = data['results']
wfs = data['wfs']
numWaveforms = wfs.size
else:
print "No saved waveforms available. Loading from Data"
exit(0)
#prep holders for each wf-specific param
r_arr = np.empty(numWaveforms)
phi_arr = np.empty(numWaveforms)
z_arr = np.empty(numWaveforms)
scale_arr = np.empty(numWaveforms)
t0_arr = np.empty(numWaveforms)
smooth_arr = np.ones(numWaveforms) * 7.
simWfArr = np.empty((1, numWaveforms, fitSamples))
#Prepare the initial value arrays
for (idx, wf) in enumerate(wfs):
wf.WindowWaveformTimepoint(fallPercentage=.99)
r_arr[idx], phi_arr[idx], z_arr[idx], scale_arr[idx], t0_arr[
idx], smooth_arr[idx] = results[idx]['x']
t0_arr[
idx] += 10 #because i had a different windowing offset back in the day
#Plot the waveforms to take a look at the initial guesses
if False:
fig = plt.figure()
for (idx, wf) in enumerate(wfs):
print "WF number %d:" % idx
print " >>r: %f\n >>phi %f\n >>z %f\n >>e %f\n >>t0 %f\n >>smooth %f" % (
r_arr[idx], phi_arr[idx], z_arr[idx], scale_arr[idx],
t0_arr[idx], smooth_arr[idx])
ml_wf = det.GetSimWaveform(r_arr[idx],
phi_arr[idx],
z_arr[idx],
scale_arr[idx] * 100,
t0_arr[idx],
fitSamples,
smoothing=smooth_arr[idx])
plt.plot(ml_wf, color="b")
plt.plot(wf.windowedWf, color="r")
value = raw_input(' --> Press q to quit, any other key to continue\n')
if value == 'q': exit(0)
#Initialize this thread's globals
initializeDetectorAndWaveforms(det, wfs)
#Initialize the multithreading
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
#Do the MCMC
mcmc_startguess = np.hstack((
r_arr[:],
phi_arr[:],
z_arr[:],
scale_arr[:] * 100.,
t0_arr[:],
smooth_arr[:], # waveform-specific params
tempGuess,
gradGuess,
pcRadGuess,
pcLenGuess,
zero_1,
pole_1,
pole_real,
pole_imag)) # detector-specific
#number of walkers _must_ be even
if nwalkers % 2:
nwalkers += 1
#Initialize walkers with a random, narrow ball around the start guess
pos0 = [
mcmc_startguess + 1e-2 * np.random.randn(ndim) * mcmc_startguess
for i in range(nwalkers)
]
#Make sure everything in the initial guess is within bounds
for pos in pos0:
pos[:numWaveforms] = np.clip(pos[:numWaveforms], 0,
np.floor(det.detector_radius * 10.) / 10.)
pos[numWaveforms:2 * numWaveforms] = np.clip(
pos[numWaveforms:2 * numWaveforms], 0, np.pi / 4)
pos[2 * numWaveforms:3 * numWaveforms] = np.clip(
pos[2 * numWaveforms:3 * numWaveforms], 0,
np.floor(det.detector_length * 10.) / 10.)
pos[4 * numWaveforms:5 * numWaveforms] = np.clip(
pos[4 * numWaveforms:5 * numWaveforms], 0, fitSamples)
pos[5 * numWaveforms:6 * numWaveforms] = np.clip(
pos[5 * numWaveforms:6 * numWaveforms], 0, 20.)
pos[tempIdx] = np.clip(pos[tempIdx], 40, 120)
pos[gradIdx] = np.clip(pos[gradIdx], det.gradList[0], det.gradList[-1])
pos[pcRadIdx] = np.clip(pos[pcRadIdx], det.pcRadList[0],
det.pcRadList[-1])
pos[pcLenIdx] = np.clip(pos[pcLenIdx], det.pcLenList[0],
det.pcLenList[-1])
prior = lnprior(pos, )
if not np.isfinite(prior):
print "BAD PRIOR WITH START GUESS YOURE KILLING ME SMALLS"
print pos
exit(0)
#Initialize, run the MCMC
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, pool=p)
#w/ progress bar, & time the thing
start = timer()
for (idx, result) in enumerate(
sampler.sample(pos0, iterations=iter, storechain=True)):
continue
end = timer()
pool.close()
print "Elapsed time: " + str(end - start)
print "Dumping chain to file..."
np.save("sampler_mpi_%dwfs.npy" % numWaveforms, sampler.chain)
print "Making MCMC steps figure..."
######### Plots for Waveform params
stepsFig = plt.figure(2, figsize=fig_size)
plt.clf()
ax0 = stepsFig.add_subplot(611)
ax1 = stepsFig.add_subplot(612, sharex=ax0)
ax2 = stepsFig.add_subplot(613, sharex=ax0)
ax3 = stepsFig.add_subplot(614, sharex=ax0)
ax4 = stepsFig.add_subplot(615, sharex=ax0)
ax5 = stepsFig.add_subplot(616, sharex=ax0)
ax0.set_ylabel('r')
ax1.set_ylabel('phi')
ax2.set_ylabel('z')
ax3.set_ylabel('scale')
ax4.set_ylabel('t0')
ax5.set_ylabel('smoothing')
for i in range(nwalkers):
for j in range(wfs.size):
ax0.plot(sampler.chain[i, :, 0 + j], alpha=0.3) # r
ax1.plot(sampler.chain[i, :, numWaveforms + j], alpha=0.3) # phi
ax2.plot(sampler.chain[i, :, 2 * numWaveforms + j], alpha=0.3) #z
ax3.plot(sampler.chain[i, :, 3 * numWaveforms + j],
alpha=0.3) #energy
ax4.plot(sampler.chain[i, :, 4 * numWaveforms + j], alpha=0.3) #t0
ax5.plot(sampler.chain[i, :, 5 * numWaveforms + j],
alpha=0.3) #smoothing
plt.savefig("emcee_mpi_wfchain_%dwfs.png" % numWaveforms)
######### Plots for Detector params
stepsFigDet = plt.figure(3, figsize=fig_size)
plt.clf()
ax0 = stepsFigDet.add_subplot(411)
ax1 = stepsFigDet.add_subplot(412, sharex=ax0)
ax2 = stepsFigDet.add_subplot(413, sharex=ax0)
ax3 = stepsFigDet.add_subplot(414, sharex=ax0)
ax0.set_ylabel('temp')
ax1.set_ylabel('grad')
ax2.set_ylabel('pcRad')
ax3.set_ylabel('pcLen')
for i in range(nwalkers):
ax0.plot(sampler.chain[i, :, tempIdx], "b", alpha=0.3) #temp
ax1.plot(sampler.chain[i, :, gradIdx], "b", alpha=0.3) #grad
ax2.plot(sampler.chain[i, :, pcRadIdx], "b", alpha=0.3) #pcrad
ax3.plot(sampler.chain[i, :, pcLenIdx], "b", alpha=0.3) #pclen
plt.savefig("emcee_mpi_detchain_%dwfs.png" % numWaveforms)
#and for the transfer function
stepsFigTF = plt.figure(4, figsize=fig_size)
plt.clf()
tf0 = stepsFigTF.add_subplot(411)
tf1 = stepsFigTF.add_subplot(412, sharex=ax0)
tf2 = stepsFigTF.add_subplot(413, sharex=ax0)
tf3 = stepsFigTF.add_subplot(414, sharex=ax0)
tf0.set_ylabel('zero_1')
tf1.set_ylabel('pole_1')
tf2.set_ylabel('pole_real')
tf3.set_ylabel('pole_imag')
for i in range(nwalkers):
tf0.plot(sampler.chain[i, :, -4], "b", alpha=0.3) #2
tf1.plot(sampler.chain[i, :, -3], "b", alpha=0.3) #den1
tf2.plot(sampler.chain[i, :, -2], "b", alpha=0.3) #2
tf3.plot(sampler.chain[i, :, -1], "b", alpha=0.3) #3
plt.savefig("emcee_mpi_tfchain_%dwfs.png" % numWaveforms)
samples = sampler.chain[:, burnIn:, :].reshape((-1, ndim))
print "temp is %f" % np.median(samples[:, tempIdx])
print "grad is %f" % np.median(samples[:, gradIdx])
print "pcrad is %f" % np.median(samples[:, pcRadIdx])
print "pclen is %f" % np.median(samples[:, pcLenIdx])
print "zero_1 is %f" % np.median(samples[:, -4])
print "pole_1 is %f" % np.median(samples[:, -3])
print "pole_real is %f" % np.median(samples[:, -2])
print "pole_imag is %f" % np.median(samples[:, -1])
#TODO: Aaaaaaand plot some waveforms..
simWfs = np.empty((wfPlotNumber, numWaveforms, fitSamples))
for idx, (theta) in enumerate(samples[np.random.randint(
len(samples), size=wfPlotNumber)]):
temp, impGrad, pcRad, pcLen = theta[tempIdx], theta[gradIdx], theta[
pcRadIdx], theta[pcLenIdx]
zero_1, pole_1, pole_real, pole_imag = theta[-4:]
r_arr, phi_arr, z_arr, scale_arr, t0_arr, smooth_arr = theta[:-8].reshape(
(6, numWaveforms))
det.SetTemperature(temp)
det.SetFields(pcRad, pcLen, impGrad)
zeros = [zero_1, 0]
poles = [
pole_real + pole_imag * 1j, pole_real - pole_imag * 1j, pole_1
]
det.SetTransferFunction(zeros, poles, 1E7)
for wf_idx in range(wfs.size):
wf_i = det.GetSimWaveform(r_arr[wf_idx], phi_arr[wf_idx],
z_arr[wf_idx], scale_arr[wf_idx],
t0_arr[wf_idx], fitSamples)
simWfs[idx, wf_idx, :] = wf_i
if wf_i is None:
print "Waveform %d, %d is None" % (idx, wf_idx)
residFig = plt.figure(4, figsize=(20, 15))
helpers.plotManyResidual(simWfs, wfs, figure=residFig)
plt.savefig("emcee_mpi_waveforms_%dwfs.png" % numWaveforms)
def mcmc(result_path, result_name, param_dict, nwalkers=10, steps=2,
output='./mcmc_chains.h5', overwrite=False, covmat=None,
redshift=0.05, logmass_min=11., logmass_max=16.):
pool = MPIPool(loadbalance=True, debug=False)
rank = pool.rank
comm = pool.comm
# initializign CAMB power spectrum
_camb.set_matter_power(redshifts=[redshift, ], kmax=3.e1)
if rank == 0:
result = h5py.File(result_path + result_name, 'r')
pksz = result['pkSZ'][:]
jk_sample = False
if 'pkSZ_random' in result.keys():
pksz_random = result['pkSZ_random'][:]
jk_sample = False
elif 'pkSZ_jk' in result.keys():
pksz_random = result['pkSZ_jk'][:]
jk_sample = True
else:
print "Need random samples"
exit()
pksz_bins = result['pkSZ_bins'][:]
d_bins = pksz_bins[1:] - pksz_bins[:-1]
pksz_bins = pksz_bins[:-1] + 0.5 * d_bins
result.close()
lin_scale = pksz_bins > 25.
pksz_obs = pksz[lin_scale]
pksz_err = None
pksz_cov = np.cov(pksz_random, rowvar=False, bias=jk_sample)
if jk_sample:
spl_n = float(pksz_random.shape[0] - 1)
bin_n = pksz_cov.shape[0]
pksz_cov *= spl_n
pksz_covm = np.linalg.inv(pksz_cov[:, lin_scale][lin_scale, :])
pksz_covm *= (spl_n - bin_n) / spl_n
else:
pksz_covm = np.linalg.inv(pksz_cov[:, lin_scale][lin_scale, :])
pksz_bins = pksz_bins[lin_scale]
else:
pksz_obs = None
pksz_err = None
pksz_bins = None
pksz_covm = None
pksz_obs = comm.bcast(pksz_obs, root=0)
#pksz_err = comm.bcast(pksz_err, root=0)
pksz_bins = comm.bcast(pksz_bins, root=0)
pksz_covm = comm.bcast(pksz_covm, root=0)
comm.barrier()
if rank != 0:
pool.wait()
sys.exit(0)
param, theta, theta_min, theta_max, param_tex, cosm_param_idx, camb_run\
= read_param_dict(param_dict, camb_param=_camb.params.keys())
paramnames = open(output.replace('.h5', '.paramnames'), 'w')
for i in range(param.shape[0]):
paramnames.write('%s\t\t'%param[i] + param_tex[i] + '\n')
paramnames.close()
# param = [cent, min, max]
#tau_bar = [1., -1., 3.]
#mnu = [0.4, 0.2, 0.6]
#ombh2 = [0.0221, 0.005, 0.1]
#omch2 = [0.12, 0.001, 0.99]
#w = [-1, -3., 1.]
#wa = [0., -3., 3.]
#theta = param
#theta_min = np.array([tau_bar[1], w[1]])
#theta_max = np.array([tau_bar[2], w[2]])
ndim = theta.shape[0]
#threads = nwalkers
threads = 1
pos = [theta + 1.e-4 * np.random.randn(ndim) for i in range(nwalkers)]
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob, threads=threads,
pool=pool, args=(pksz_bins, pksz_obs, pksz_err, pksz_covm, param),
kwargs={ 'theta_min' :theta_min,
'theta_max' :theta_max,
'cosm_param_idx' :cosm_param_idx,
'camb_run' :camb_run,
'T_CMB' :2.7255,
'logmass_min' :logmass_min,
'logmass_max' :logmass_max})
# Run 100 steps as a burn-in.
#pos, prob, state = sampler.run_mcmc(pos, 100)
# Reset the chain to remove the burn-in samples.
#sampler.reset()
# Starting from the final position in the burn-in chain
#sampler.run_mcmc(pos, steps, rstate0=state)
#chain = np.zeros((size, ) + chain_local.shape )
#comm.Gather(chain_local, chain, root=0)
step_group = 100
if step_group > steps: step_group = steps
n_steps = steps / step_group
state = None
if rank == 0:
if overwrite or not os.path.exists(output):
mcmc_chains = h5py.File(output, 'w')
#mcmc_chains['n_steps'] = n_steps
mcmc_chains['n_steps'] = 0
mcmc_chains['pos'] = pos
if covmat is not None:
mcmc_chains['covmat'] = np.zeros((ndim, ndim))
#mcmc_chains['state'] = 0
n_steps0 = 0
mcmc_chains.close()
else:
mcmc_chains = h5py.File(output, 'a')
n_steps0 = mcmc_chains['n_steps'][...]
pos = mcmc_chains['pos'][...]
if covmat is not None and n_steps0 != 0:
covmat = mcmc_chains['covmat']
#state = mcmc_chains['state'][...]
#if state == 0: state = None
mcmc_chains.close()
for i in range(n_steps0, n_steps0 + n_steps):
if rank == 0:
t1 = time.time()
if covmat is not None:
mh_proposal = MH_proposal(covmat, sampler._random)
else:
mh_proposal = None
#mh_proposal = None
pos, prob, state = sampler.run_mcmc(pos, step_group, state,
mh_proposal=mh_proposal)
if rank == 0:
chain = sampler.chain
chisq = sampler.lnprobability * (-2.)
mcmc_chains = h5py.File(output, 'a')
mcmc_chains['chains_%02d'%i] = chain
mcmc_chains['chisqs_%02d'%i] = chisq
mcmc_chains['n_steps'][...] = i + 1
mcmc_chains['pos'][...] = pos
#mcmc_chains['state'][...] = state
#pksz_covm = np.cov(pksz_random[:, lin_scale], rowvar=False)
if covmat is not None:
covmat = np.cov(chain.reshape(-1, chain.shape[-1]), rowvar=False)
mcmc_chains['covmat'][...] = covmat
mcmc_chains.close()
print "[TIMING] %3d x %4d Steps: %8.4f [s]"\
%(nwalkers, step_group, time.time() - t1)
print "Mean acceptance fraction: ", np.mean(sampler.acceptance_fraction)
sampler.reset()
pool.close()
sampler.sample(burninPos,
lnprob0=burninProb,
rstate0=burninRstate,
iterations=mcIterations)):
#if (i+1)%2 == 0:
# print("{0:5.1%}".format(float(i)/mcIterations))
print('running step {0} of {1} in main chain'.format(i, mcIterations))
fout = open('mainchain.dat', 'a')
pos = samplerResult[0]
prob = samplerResult[1]
for k in range(pos.shape[0]):
fout.write("{0} {1} {2}\n".format(k, pos[k], prob[k]))
fout.close()
if useMPI:
processPool.close()
samples = sampler.chain[:, :, :].reshape((-1, nDim))
if not e0_only:
# Compute the quantiles.
# this comes from https://github.com/dfm/emcee/blob/master/examples/line.py
quartileResults = map(lambda v: (v[1], v[2] - v[1], v[1] - v[0]),
zip(*np.percentile(samples, [16, 50, 84], axis=0)))
ed_mcmc, loc_mcmc, scale_mcmc, s_mcmc = quartileResults[:4]
print("""MCMC result:
E_D initial = {0[0]} +{0[1]} -{0[2]}
loc = {1[0]} +{1[1]} -{1[2]}
scale = {2[0]} + {2[1]} - {2[2]}
s = {3[0]} + {3[1]} - {3[2]}
def main(runmpi=False, nw=100, th=6, bi=10, fr=10):
if runmpi:
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
else:
pool=None
time, flux, ferr = get_lc()
toi = 175
cadence = 120
rho = 18
rho_unc = 1
nplanets = 3
ld1 = 0.1642
ld2 = 0.4259
dil=0.0
periods = [2.25321888449, 3.6906274382, 7.45131144274]
impacts = [0.26, 0.21, 0.89]
T0s = [1354.90455205, 1356.203624274, 1355.2866249]
rprss = [0.02011, 0.038564, 0.0438550698]
planet_guess = np.array([])
for i in range(nplanets):
planet_guess = np.r_[planet_guess,
T0s[i], periods[i], impacts[i], rprss[i],
0.0, 0.0
]
nwalkers = nw
threads = th
burnin = bi
fullrun = fr
thin = 1
M = tmod.transitmc2(
nplanets, cadence)
M.get_ld(ld1, ld2)
M.already_open(time,
flux, ferr)
M.get_rho([rho, rho_unc])
M.get_zpt(0.0)
M.get_sol(*planet_guess)
outfile = 'koi{0}_np{1}.hdf5'.format(
toi, nplanets)
p0 = M.get_guess(nwalkers)
l_var = np.shape(p0)[1]
tom = tmod.logchi2
args = [M.nplanets, M.rho_0, M.rho_0_unc,
M.ld1, M.ld1_unc, M.ld2, M.ld2_unc,
M.flux, M.err,
M.fixed_sol,
M.time, M._itime, M._ntt,
M._tobs, M._omc, M._datatype]
N = len([indval for indval in range(fullrun)
if indval%thin == 0])
with h5py.File(outfile, u"w") as f:
f.create_dataset("time", data=M.time)
f.create_dataset("flux", data=M.flux)
f.create_dataset("err", data=M.err)
f.attrs["rho_0"] = M.rho_0
f.attrs["rho_0_unc"] = M.rho_0_unc
f.attrs["nplanets"] = M.nplanets
f.attrs["ld1"] = M.ld1
f.attrs["ld2"] = M.ld2
g = f.create_group("mcmc")
g.attrs["nwalkers"] = nwalkers
g.attrs["burnin"] = burnin
g.attrs["iterations"] = fullrun
g.attrs["thin"] = thin
g.create_dataset("fixed_sol", data= M.fixed_sol)
g.create_dataset("fit_sol_0", data= M.fit_sol_0)
c_ds = g.create_dataset("chain",
(nwalkers, N, l_var),
dtype=np.float64)
lp_ds = g.create_dataset("lnprob",
(nwalkers, N),
dtype=np.float64)
if runmpi:
sampler = emcee.EnsembleSampler(nwalkers, l_var, tom,
args=args,pool=pool)
else:
sampler = emcee.EnsembleSampler(nwalkers, l_var, tom,
args=args,threads=th)
time1 = thetime.time()
p2, prob, state = sampler.run_mcmc(p0, burnin,
storechain=False)
sampler.reset()
with h5py.File(outfile, u"a") as f:
g = f["mcmc"]
g.create_dataset("burnin_pos", data=p2)
g.create_dataset("burnin_prob", data=prob)
time2 = thetime.time()
print('burn-in took ' + str((time2 - time1)/60.) + ' min')
time1 = thetime.time()
for i, (pos, lnprob, state) in enumerate(tqdm(sampler.sample(p2,
iterations=fullrun, rstate0=state,
storechain=False), total=fullrun)):
#do the thinning in the loop here
if i % thin == 0:
ind = i / thin
with h5py.File(outfile, u"a") as f:
g = f["mcmc"]
c_ds = g["chain"]
lp_ds = g["lnprob"]
c_ds[:, ind, :] = pos
lp_ds[:, ind] = lnprob
time2 = thetime.time()
print('MCMC run took ' + str((time2 - time1)/60.) + ' min')
print('')
print("Mean acceptance: "
+ str(np.mean(sampler.acceptance_fraction)))
print('')
if runmpi:
pool.close()
else:
sampler.pool.close()
return sampler
def run_emcee_seeded(light_curve, transit_params, spot_parameters, n_steps,
n_walkers, output_path, burnin=0.7,
n_extra_spots=1, skip_priors=False):
"""
Fit for transit depth and spot parameters given initial guess informed by
results from `peak_finder`
Parameters
----------
light_curve : `friedrich.lightcurve.TransitLightCurve`
Light curve to fit
transit_params : `~batman.TransitParams`
Transit light curve parameters
spot_parameters : list
List of all spot parameters in [amp, t0, sig, amp, t0, sig, ...] order
n_steps : int
Number of MCMC steps to take
n_walkers : int
Number of MCMC walkers to initialize (must be even, more than twice the
number of free params in fit)
output_path : str
Path to HDF5 archive output for storing results
burnin : float
Fraction of total number of steps to save to output (will truncate
the first `burnin` of the light curve)
n_extra_spots : int
Add `n_extra_spots` extra spots to the fit to soak up spots not
predicted by `peak_finder`
skip_priors : bool
Should a prior be applied to the depth parameter?
Returns
-------
sampler : `emcee.EnsembleSampler`
Sampler object returned by `emcee`
"""
times = light_curve.times.jd
fluxes = light_curve.fluxes
errors = light_curve.errors
lower_t_bound, upper_t_bound = get_in_transit_bounds(times, transit_params)
amps = spot_parameters[::3]
init_depth = transit_params.rp**2
extra_spot_params = [0.1*np.min(amps), np.mean(times),
0.05*(upper_t_bound-lower_t_bound)]
fit_params = np.concatenate([spot_parameters,
n_extra_spots*extra_spot_params])
ndim, nwalkers = len(fit_params), n_walkers
pos = []
while len(pos) < nwalkers:
realization = fit_params + 1e-5*np.random.randn(ndim)
if not np.isinf(lnprior(realization, fluxes, lower_t_bound,
upper_t_bound, transit_params, skip_priors)):
pos.append(realization)
print('Begin MCMC...')
pool = MPIPool(loadbalance=True)
if not pool.is_master():
pool.wait()
sys.exit(0)
sampler = emcee.EnsembleSampler(nwalkers, ndim, lnprob,
args=(times, fluxes, errors, lower_t_bound,
upper_t_bound, transit_params,
skip_priors),
pool=pool)
sampler.run_mcmc(pos, n_steps)
print('Finished MCMC...')
pool.close()
burnin_len = int(burnin*n_steps)
from .storage import create_results_archive
create_results_archive(output_path, light_curve, sampler, burnin_len, ndim)
return sampler
### skips if files do not exist for some reason
print 'Warning: file does not exist, cosmo, snap'
return
if os.path.isfile(out_fn): ###### in case the code breaks
return
######### read rockstar files
print 'Opening rockstar files:', rockstar_fn
reader = sim_manager.TabularAsciiReader(rockstar_fn, columns_to_keep_dict)
rock_arr = reader.read_ascii()
logM = log10(rock_arr['halo_mvir'])
rock_arr = 0 ## release memory
hmf = histogram(logM, bins=hist_bins)[0]
save(out_fn, hmf)
all_snaps = []
for i in range(len(cosmo_arr)):
for isnap in arange(30, nsnaps_arr[i]):
all_snaps.append([cosmo_arr[i], int(isnap)])
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
pool.map(Phm_gen, all_snaps)
#pool.map(Phh_gen, all_snaps)
#pool.map(hmf_gen, all_snaps)
pool.close()
def mcmc_mpi(Nwalkers,
Nchains,
observables=['nbar', 'xi'],
data_dict={
'Mr': 21,
'b_normal': 0.25
},
prior_name='first_try',
mcmcrun=None):
'''
Standard MCMC implementaion
Parameters
-----------
- Nwalker :
Number of walkers
- Nchains :
Number of MCMC chains
- observables :
list of observables. Options are: ['nbar','xi'],['nbar','gmf'],['xi']
- data_dict : dictionary that specifies the observation keywords
'''
#Initializing the vector of observables and inverse covariance matrix
if observables == ['xi']:
fake_obs = Data.data_xi(**data_dict)
#fake_obs_icov = Data.data_inv_cov('xi', **data_dict)
fake_obs_icov = Data.data_cov(inference='mcmc', **data_dict)[1:16,
1:16]
if observables == ['nbar', 'xi']:
fake_obs = np.hstack(
[Data.data_nbar(**data_dict),
Data.data_xi(**data_dict)])
fake_obs_icov = Data.data_cov(inference='mcmc', **data_dict)[:16, :16]
if observables == ['nbar', 'gmf']:
##### FIRST BIN OF GMF DROPPED ###############
# CAUTION: hardcoded
fake_obs = np.hstack(
[Data.data_nbar(**data_dict),
Data.data_gmf(**data_dict)[1:]])
fake_obs_icov = np.zeros((10, 10))
#print Data.data_cov(**data_dict)[17: , 17:].shape
# Covariance matrix being adjusted accordingly
fake_obs_icov[1:, 1:] = Data.data_cov(inference='mcmc',
**data_dict)[17:, 17:]
fake_obs_icov[0, 1:] = Data.data_cov(inference='mcmc',
**data_dict)[0, 17:]
fake_obs_icov[1:, 0] = Data.data_cov(inference='mcmc',
**data_dict)[17:, 0]
fake_obs_icov[0, 0] = Data.data_cov(inference='mcmc', **data_dict)[0,
0]
# True HOD parameters
data_hod_dict = Data.data_hod_param(Mr=data_dict['Mr'])
data_hod = np.array([
data_hod_dict['logM0'], # log M0
np.log(data_hod_dict['sigma_logM']), # log(sigma)
data_hod_dict['logMmin'], # log Mmin
data_hod_dict['alpha'], # alpha
data_hod_dict['logM1'] # log M1
])
Ndim = len(data_hod)
# Priors
prior_min, prior_max = PriorRange(prior_name)
prior_range = np.zeros((len(prior_min), 2))
prior_range[:, 0] = prior_min
prior_range[:, 1] = prior_max
# mcmc chain output file
chain_file = ''.join([
util.mcmc_dir(),
util.observable_id_flag(observables), '.', mcmcrun, '.mcmc_chain.dat'
])
#print chain_file
if os.path.isfile(chain_file) and continue_chain:
print 'Continuing previous MCMC chain!'
sample = np.loadtxt(chain_file)
Nchain = Niter - (len(sample) / Nwalkers
) # Number of chains left to finish
if Nchain > 0:
pass
else:
raise ValueError
print Nchain, ' iterations left to finish'
# Initializing Walkers from the end of the chain
pos0 = sample[-Nwalkers:]
else:
# new chain
f = open(chain_file, 'w')
f.close()
Nchain = Niter
# Initializing Walkers
random_guess = data_hod
pos0 = np.repeat(random_guess, Nwalkers).reshape(Ndim, Nwalkers).T + \
5.e-2 * np.random.randn(Ndim * Nwalkers).reshape(Nwalkers, Ndim)
#print pos0.shape
# Initializing MPIPool
pool = MPIPool()
if not pool.is_master():
pool.wait()
sys.exit(0)
# Initializing the emcee sampler
hod_kwargs = {
'prior_range': prior_range,
'data': fake_obs,
'data_icov': fake_obs_icov,
'observables': observables,
'Mr': data_dict['Mr']
}
sampler = emcee.EnsembleSampler(Nwalkers,
Ndim,
lnPost,
pool=pool,
kwargs=hod_kwargs)
# Initializing Walkers
for result in sampler.sample(pos0, iterations=Nchain, storechain=False):
position = result[0]
#print position
f = open(chain_file, 'a')
for k in range(position.shape[0]):
output_str = '\t'.join(position[k].astype('str')) + '\n'
f.write(output_str)
f.close()
pool.close()
