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Commit 9224e741 authored by Gregory Ashton's avatar Gregory Ashton
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Various improvements to generate pub. quality tables and plots

parent d6edafae
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examples/fully_coherent_search_using_MCMC.py
View file @ 9224e741
......@@ -18,7 +18,7 @@ theta_prior = {'F0': {'type': 'unif', 'lower': F0*(1-1e-6), 'upper': F0*(1+1e-6)
'Delta': Delta
}
ntemps = 4
ntemps = 3
log10temperature_min = -1
nwalkers = 100
nsteps = [1000, 1000]
......
examples/grided_frequency_search.py 0 → 100644
View file @ 9224e741
import pyfstat
import numpy as np
import matplotlib.pyplot as plt
plt.style.use('paper')
F0 = 30.0
F1 = 0
F2 = 0
Alpha = 1.0
Delta = 1.5
# Properties of the GW data
sqrtSX = 1e-23
tstart = 1000000000
duration = 100*86400
tend = tstart+duration
tref = .5*(tstart+tend)
depth = 70
data_label = 'grided_frequency_depth_{:1.0f}'.format(depth)
h0 = sqrtSX / depth
data = pyfstat.Writer(
label=data_label, outdir='data', tref=tref,
tstart=tstart, F0=F0, F1=F1, F2=F2, duration=duration, Alpha=Alpha,
Delta=Delta, h0=h0, sqrtSX=sqrtSX)
data.make_data()
m = 0.001
dF0 = np.sqrt(12*m)/(np.pi*duration)
DeltaF0 = 800*dF0
F0s = [F0-DeltaF0/2., F0+DeltaF0/2., dF0]
F1s = [F1]
F2s = [F2]
Alphas = [Alpha]
Deltas = [Delta]
search = pyfstat.GridSearch(
'grided_frequency_search', 'data', 'data/*'+data_label+'*sft', F0s, F1s,
F2s, Alphas, Deltas, tref, tstart, tend)
search.run()
fig, ax = plt.subplots()
xidx = search.keys.index('F0')
frequencies = np.unique(search.data[:, xidx])
twoF = search.data[:, -1]
#mismatch = np.sign(x-F0)*(duration * np.pi * (x - F0))**2 / 12.0
ax.plot(frequencies, twoF, 'k', lw=1)
DeltaF = frequencies - F0
sinc = np.sin(np.pi*DeltaF*duration)/(np.pi*DeltaF*duration)
A = np.abs((np.max(twoF)-4)*sinc**2 + 4)
ax.plot(frequencies, A, '-r', lw=1)
ax.set_ylabel('$\widetilde{2\mathcal{F}}$')
ax.set_xlabel('Frequency')
ax.set_xlim(F0s[0], F0s[1])
dF0 = np.sqrt(12*1)/(np.pi*duration)
xticks = [F0-10*dF0, F0, F0+10*dF0]
ax.set_xticks(xticks)
xticklabels = ['$f_0 {-} 10\Delta f$', '$f_0$', '$f_0 {+} 10\Delta f$']
ax.set_xticklabels(xticklabels)
plt.tight_layout()
fig.savefig('{}/{}_1D.png'.format(search.outdir, search.label), dpi=300)
examples/weak_signal_follow_up.py
View file @ 9224e741
import pyfstat
# Define parameters of the Crab pulsar as an example
F0 = 30.0
F1 = -1e-10
F1 = 0
F2 = 0
Alpha = 5e-3
Delta = 6e-2
tref = 362750407.0
Alpha = 1.0
Delta = 0.5
# Properties of the GW data
sqrtSX = 1e-23
tstart = 1000000000
duration = 100*86400
tend = tstart+duration
tref = .5*(tstart+tend)
depth = 50
depth = 70
data_label = 'weak_signal_follow_up_depth_{:1.0f}'.format(depth)
h0 = sqrtSX / depth
data = pyfstat.Writer(
label='depth_{:1.0f}'.format(depth), outdir='data', tref=tref,
label=data_label, outdir='data', tref=tref,
tstart=tstart, F0=F0, F1=F1, F2=F2, duration=duration, Alpha=Alpha,
Delta=Delta, h0=h0, sqrtSX=sqrtSX)
data.make_data()
......@@ -29,35 +29,40 @@ twoF = data.predict_fstat()
print 'Predicted twoF value: {}\n'.format(twoF)
# Search
theta_prior = {'F0': {'type': 'unif', 'lower': F0*(1-1e-4),
'upper': F0*(1+1e-4)},
'F1': {'type': 'unif', 'lower': F1*(1+1e-2),
'upper': F1*(1-1e-2)},
theta_prior = {'F0': {'type': 'unif', 'lower': F0*(1-1e-6),
'upper': F0*(1+1e-6)},
'F1': F1, #{'type': 'unif', 'lower': F1*(1+1e-2),
#'upper': F1*(1-1e-2)},
'F2': F2,
'Alpha': {'type': 'unif', 'lower': Alpha-1e-2,
'upper': Alpha+1e-2},
'Delta': {'type': 'unif', 'lower': Delta-5e-2,
'upper': Delta+5e-2},
'Delta': {'type': 'unif', 'lower': Delta-1e-2,
'upper': Delta+1e-2},
}
ntemps = 1
ntemps = 3
log10temperature_min = -1
nwalkers = 100
run_setup = [(1000, 50),
(1000, 30),
(1000, 20),
(1000, 15),
(1000, 10),
(1000, 5),
(1000, 1),
((1000, 1000), 1, True)]
nwalkers = 200
scatter_val = 1e-10
stages = 7
steps = 100
#run_setup = [(steps, 2**i) for i in reversed(range(1, stages+1))]
#run_setup.append(((steps, steps), 1, True))
run_setup = [(steps, 80),
(steps, 40),
(steps, 20),
(steps, 10),
(steps, 5),
((steps, steps), 1, False)]
mcmc = pyfstat.MCMCFollowUpSearch(
label='weak_signal_follow_up', outdir='data',
sftfilepath='data/*depth*sft', theta_prior=theta_prior, tref=tref,
sftfilepath='data/*'+data_label+'*sft', theta_prior=theta_prior, tref=tref,
minStartTime=tstart, maxStartTime=tend, nwalkers=nwalkers,
ntemps=ntemps, log10temperature_min=log10temperature_min)
ntemps=ntemps, log10temperature_min=log10temperature_min,
scatter_val=scatter_val)
mcmc.run(run_setup)
mcmc.plot_corner(add_prior=True)
mcmc.print_summary()
mcmc.generate_loudest()
#mcmc.generate_loudest()
pyfstat.py
View file @ 9224e741
......@@ -70,6 +70,26 @@ stream_handler.setFormatter(logging.Formatter(
logger.addHandler(stream_handler)
def round_to_n(x, n):
if not x:
return 0
power = -int(np.floor(np.log10(abs(x)))) + (n - 1)
factor = (10 ** power)
return round(x * factor) / factor
def texify_float(x, d=1):
x = round_to_n(x, d)
if 0.01 < abs(x) < 100:
return str(x)
else:
power = int(np.floor(np.log10(abs(x))))
stem = np.round(x / 10**power, d)
if d == 1:
stem = int(stem)
return r'${}{{\times}}10^{{{}}}$'.format(stem, power)
def initializer(func):
""" Decorator function to automatically assign the parameters to self """
names, varargs, keywords, defaults = inspect.getargspec(func)
......@@ -902,7 +922,7 @@ class MCMCSearch(BaseSearchClass):
pass
return sampler
def run(self, proposal_scale_factor=2):
def run(self, proposal_scale_factor=2, **kwargs):
self.old_data_is_okay_to_use = self.check_old_data_is_okay_to_use()
if self.old_data_is_okay_to_use is True:
......@@ -936,9 +956,10 @@ class MCMCSearch(BaseSearchClass):
if self.ntemps > 1:
logging.info("Tswap acceptance fraction: {}"
.format(sampler.tswap_acceptance_fraction))
fig, axes = self.plot_walkers(sampler, symbols=self.theta_symbols)
fig, axes = self.plot_walkers(sampler, symbols=self.theta_symbols,
**kwargs)
fig.savefig('{}/{}_init_{}_walkers.png'.format(
self.outdir, self.label, j))
self.outdir, self.label, j), dpi=200)
p0 = self.get_new_p0(sampler)
p0 = self.apply_corrections_to_p0(p0)
......@@ -960,8 +981,9 @@ class MCMCSearch(BaseSearchClass):
.format(sampler.tswap_acceptance_fraction))
fig, axes = self.plot_walkers(sampler, symbols=self.theta_symbols,
burnin_idx=nburn)
fig.savefig('{}/{}_walkers.png'.format(self.outdir, self.label))
burnin_idx=nburn, **kwargs)
fig.savefig('{}/{}_walkers.png'.format(self.outdir, self.label),
dpi=200)
samples = sampler.chain[0, :, nburn:, :].reshape((-1, self.ndim))
lnprobs = sampler.lnprobability[0, :, nburn:].reshape((-1))
......@@ -1200,7 +1222,8 @@ class MCMCSearch(BaseSearchClass):
def plot_walkers(self, sampler, symbols=None, alpha=0.4, color="k", temp=0,
lw=0.1, burnin_idx=None, add_det_stat_burnin=False,
fig=None, axes=None, xoffset=0, plot_det_stat=True):
fig=None, axes=None, xoffset=0, plot_det_stat=True,
context='classic'):
""" Plot all the chains from a sampler """
shape = sampler.chain.shape
......@@ -1216,7 +1239,7 @@ class MCMCSearch(BaseSearchClass):
"available range").format(temp))
chain = sampler.chain[temp, :, :, :]
with plt.style.context(('classic')):
with plt.style.context((context)):
if fig is None and axes is None:
fig = plt.figure(figsize=(8, 4*ndim))
ax = fig.add_subplot(ndim+1, 1, 1)
......@@ -1227,6 +1250,8 @@ class MCMCSearch(BaseSearchClass):
if ndim > 1:
for i in range(ndim):
axes[i].ticklabel_format(useOffset=False, axis='y')
if i < ndim:
axes[i].set_xticklabels([])
cs = chain[:, :, i].T
if burnin_idx:
axes[i].plot(xoffset+idxs[:burnin_idx],
......@@ -1247,31 +1272,33 @@ class MCMCSearch(BaseSearchClass):
if symbols:
axes[0].set_ylabel(symbols[0])
if len(axes) == ndim:
axes.append(fig.add_subplot(ndim+1, 1, ndim+1))
if plot_det_stat:
lnl = sampler.lnlikelihood[temp, :, :]
if burnin_idx and add_det_stat_burnin:
burn_in_vals = lnl[:, :burnin_idx].flatten()
axes[-1].hist(burn_in_vals[~np.isnan(burn_in_vals)], bins=50,
histtype='step', color='r')
else:
burn_in_vals = []
prod_vals = lnl[:, burnin_idx:].flatten()
axes[-1].hist(prod_vals[~np.isnan(prod_vals)], bins=50,
histtype='step', color='k')
if self.BSGL:
axes[-1].set_xlabel(r'$\mathcal{B}_\mathrm{S/GL}$')
else:
axes[-1].set_xlabel(r'$2\mathcal{F}$')
combined_vals = np.append(burn_in_vals, prod_vals)
if len(combined_vals) > 0:
minv = np.min(combined_vals)
maxv = np.max(combined_vals)
Range = abs(maxv-minv)
axes[-1].set_xlim(minv-0.1*Range, maxv+0.1*Range)
if len(axes) == ndim:
axes.append(fig.add_subplot(ndim+1, 1, ndim+1))
if plot_det_stat:
lnl = sampler.lnlikelihood[temp, :, :]
if burnin_idx and add_det_stat_burnin:
burn_in_vals = lnl[:, :burnin_idx].flatten()
axes[-1].hist(burn_in_vals[~np.isnan(burn_in_vals)], bins=50,
histtype='step', color='r')
else:
burn_in_vals = []
prod_vals = lnl[:, burnin_idx:].flatten()
axes[-1].hist(prod_vals[~np.isnan(prod_vals)], bins=50,
histtype='step', color='k')
if self.BSGL:
axes[-1].set_xlabel(r'$\mathcal{B}_\mathrm{S/GL}$')
else:
axes[-1].set_xlabel(r'$\widetilde{2\mathcal{F}}$')
axes[-1].set_ylabel(r'$\textrm{Counts}$')
combined_vals = np.append(burn_in_vals, prod_vals)
if len(combined_vals) > 0:
minv = np.min(combined_vals)
maxv = np.max(combined_vals)
Range = abs(maxv-minv)
axes[-1].set_xlim(minv-0.1*Range, maxv+0.1*Range)
axes[-2].set_xlabel(r'$\textrm{Number of steps}$', labelpad=0.1)
return fig, axes
def apply_corrections_to_p0(self, p0):
......@@ -1970,6 +1997,7 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
return .5*(prior[key]['upper'] + prior[key]['lower'])
def get_number_of_templates_estimate(self, nsegs):
""" Returns V, Vsky, Vf estimated from the super-sky metric """
tboundaries = np.linspace(self.minStartTime, self.maxStartTime,
nsegs+1)
if 'Alpha' in self.theta_keys:
......@@ -2016,30 +2044,17 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
SSkyMetric.semi_rssky_metric.data[:2, :2]))
sqrtdetG_F = np.sqrt(np.linalg.det(
SSkyMetric.semi_rssky_metric.data[2:, 2:]))
return '{:1.0e} = 1/2 x {:1.0e} x {:1.0e}'.format(
.5*sqrtdetG_SKY*sqrtdetG_F*DeltaOmega*DeltaF1*DeltaF0,
sqrtdetG_SKY*DeltaOmega,
return (.5*sqrtdetG_SKY*sqrtdetG_F*DeltaOmega*DeltaF1*DeltaF0,
.5*sqrtdetG_SKY*DeltaOmega,
sqrtdetG_F*DeltaF1*DeltaF0)
except RuntimeError:
return 'N/A'
elif self.theta_keys == ['F0', 'F1']:
return 'N/A'
def run(self, run_setup, proposal_scale_factor=2):
""" Run the follow-up with the given run_setup
Parameters
----------
run_setup: list of tuples
"""
self.nsegs = 1
self.inititate_search_object()
logging.info('Using run-setup as follow:')
logging.info('Stage | nburn | nprod | nsegs | resetp0 |'
'# templates = # sky x # Freq')
def init_run_setup(self, run_setup, log_table=True, gen_tex_table=True):
logging.info('Calculating the number of templates for this setup..')
number_of_templates = []
for i, rs in enumerate(run_setup):
rs = list(rs)
if len(rs) == 2:
......@@ -2047,17 +2062,67 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
if np.shape(rs[0]) == ():
rs[0] = (rs[0], 0)
run_setup[i] = rs
N = self.get_number_of_templates_estimate(rs[1])
logging.info('{} | {} | {} | {} | {} | {}'.format(
str(i).ljust(5), str(rs[0][0]).ljust(5),
str(rs[0][1]).ljust(5), str(rs[1]).ljust(5),
str(rs[2]).ljust(7), N))
number_of_templates.append(
self.get_number_of_templates_estimate(rs[1]))
if log_table:
logging.info('Using run-setup as follow:')
logging.info('Stage | nburn | nprod | nsegs | resetp0 |'
'# templates = # sky x # Freq')
for i, rs in enumerate(run_setup):
if number_of_templates[i] != 'N/A':
vtext = '{:1.0e} = {:1.0e} x {:1.0e}'.format(
*number_of_templates[i])
else:
vtext = number_of_templates[i]
logging.info('{} | {} | {} | {} | {} | {}'.format(
str(i).ljust(5), str(rs[0][0]).ljust(5),
str(rs[0][1]).ljust(5), str(rs[1]).ljust(5),
str(rs[2]).ljust(7), vtext))
if gen_tex_table:
filename = '{}/{}_run_setup.tex'.format(self.outdir, self.label)
with open(filename, 'w+') as f:
f.write(r'\begin{tabular}{c|cccccc}' + '\n')
f.write(r'Stage & $\Nseg$ & $\Tcoh^{\rm days}$ &'
r'$\Nsteps$ & $\V$ & $\Vsky$ & $\Vf$ \\ \hline'
'\n')
for i, rs in enumerate(run_setup):
Tcoh = (self.maxStartTime - self.minStartTime) / rs[1] / 86400
line = r'{} & {} & {} & {} & {} & {} & {} \\' + '\n'
if number_of_templates[i] == 'N/A':
V = Vsky = Vf = 'N/A'
else:
V, Vsky, Vf = number_of_templates[i]
if rs[0][-1] == 0:
nsteps = rs[0][0]
else:
nsteps = '{},{}'.format(*rs[0])
line = line.format(i, rs[1], Tcoh, nsteps,
texify_float(V), texify_float(Vsky),
texify_float(Vf))
f.write(line)
f.write(r'\end{tabular}' + '\n')
if args.setup_only:
logging.info("Exit as requested by setup_only flag")
sys.exit()
else:
return run_setup
def run(self, run_setup, proposal_scale_factor=2, **kwargs):
""" Run the follow-up with the given run_setup
Parameters
----------
run_setup: list of tuples
"""
self.nsegs = 1
self.inititate_search_object()
self.run_setup = self.init_run_setup(run_setup)
self.run_setup = run_setup
self.old_data_is_okay_to_use = self.check_old_data_is_okay_to_use()
if self.old_data_is_okay_to_use is True:
logging.warning('Using saved data from {}'.format(
......@@ -2109,18 +2174,19 @@ class MCMCFollowUpSearch(MCMCSemiCoherentSearch):
fig, axes = self.plot_walkers(sampler, symbols=self.theta_symbols,
fig=fig, axes=axes, burnin_idx=nburn,
xoffset=nsteps_total)
yvals = axes[0].get_ylim()
axes[0].annotate(
r'$T_{{\rm coh}}^{{\rm (days)}}{{=}}{:1.1f}$'.format(Tcoh),
xy=(nsteps_total, yvals[0]*(1+1e-2*(yvals[1]-yvals[0])/yvals[1])),
fontsize=6)
xoffset=nsteps_total, **kwargs)
#yvals = axes[0].get_ylim()
#axes[0].annotate(
# #r'$T_{{\rm coh}}^{{\rm (days)}}{{=}}{:1.1f}$'.format(Tcoh),
# r'{}'.format(j),
# xy=(nsteps_total, yvals[0]*(1+1e-2*(yvals[1]-yvals[0])/yvals[1])),
# fontsize=6)
for ax in axes[:-1]:
ax.axvline(nsteps_total, color='k', ls='--')
nsteps_total += nburn+nprod
fig.savefig('{}/{}_walkers.png'.format(
self.outdir, self.label), dpi=600)
self.outdir, self.label), dpi=200)
samples = sampler.chain[0, :, nburn:, :].reshape((-1, self.ndim))
lnprobs = sampler.lnprobability[0, :, nburn:].reshape((-1))
......@@ -2174,8 +2240,6 @@ class MCMCTransientSearch(MCMCSearch):
self.theta_keys = []
fixed_theta_dict = {}
self.theta_prior.pop('tstart')
self.theta_prior.pop('tend')
for key, val in self.theta_prior.iteritems():
if type(val) is dict:
fixed_theta_dict[key] = 0
......
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