def main(config_file):
# read configuration from a YAML file
config = io.read_config(config_file)
output_path = os.path.join(config["output_path"], "diagnostics")
cache_path = os.path.join(config["output_path"],"cache")
if not os.path.exists(output_path):
os.mkdir(output_path)
for filename in glob.glob(os.path.join(cache_path,"inference_*.hdf5")):
with h5py.File(filename, "r") as f:
try:
chain = np.hstack((chain,f["chain"].value))
except NameError:
chain = f["chain"].value
accfr = f["acceptance_fraction"].value
_a = (np.min(accfr),np.median(accfr),np.max(accfr))
print("min, median, max: {}, {}, {}".format(*_a))
acf = autocorr.function(np.mean(chain, axis=0), axis=0)
plt.clf()
for ii in range(4):
plt.plot(acf[:,ii], marker=None, alpha=0.75)
plt.savefig(os.path.join(output_path, "acf.png"))
def main(config_file):
# read configuration from a YAML file
config = io.read_config(config_file)
output_path = os.path.join(config["output_path"], "diagnostics")
cache_path = os.path.join(config["output_path"], "cache")
if not os.path.exists(output_path):
os.mkdir(output_path)
for filename in glob.glob(os.path.join(cache_path, "inference_*.hdf5")):
with h5py.File(filename, "r") as f:
try:
chain = np.hstack((chain, f["chain"].value))
except NameError:
chain = f["chain"].value
accfr = f["acceptance_fraction"].value
_a = (np.min(accfr), np.median(accfr), np.max(accfr))
print("min, median, max: {}, {}, {}".format(*_a))
acf = autocorr.function(np.mean(chain, axis=0), axis=0)
plt.clf()
for ii in range(4):
plt.plot(acf[:, ii], marker=None, alpha=0.75)
plt.savefig(os.path.join(output_path, "acf.png"))
def test_coordinate_constraints(self):
""" Want to test that having a missing dimension, other coordinates
place constraints on the missing one.
"""
test_path = os.path.join(output_path, "model", "coords")
if not os.path.exists(test_path):
os.mkdir(test_path)
ptc_params = """
parameters: [l,b,d,mul,mub,vr]
missing_dims: [l,b,d,mul,mub,vr]
"""
sat_params = """
parameters: [l,b,d,mul,mub,vr]
missing_dims: [l,b,d,mul,mub,vr]
"""
_config = minimum_config.format(potential_params="",
particles_params=ptc_params,
satellite_params=sat_params)
config = io.read_config(_config)
model = si.StreamModel.from_config(config)
model.sample_priors()
ix = -3
truth = model.truths[ix]
vals = np.linspace(-0.02, 0., Nfine)
#vals = np.linspace(-0.012,-0.003,Nfine)
Ls = []
for val in vals:
p = model.truths.copy()
p[ix] = val
Ls.append(model(p))
Ls = np.array(Ls)
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
ax.plot(vals, Ls, marker=None, linestyle='-')
ax.axvline(truth)
fig.savefig(os.path.join(test_path, "{}.png".format("mul")))
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
ax.plot(vals, np.exp(Ls - np.max(Ls)), marker=None, linestyle='-')
ax.axvline(truth)
fig.savefig(os.path.join(test_path, "{}_exp.png".format("mul")))
def test_coordinate_constraints(self):
""" Want to test that having a missing dimension, other coordinates
place constraints on the missing one.
"""
test_path = os.path.join(output_path, "model", "coords")
if not os.path.exists(test_path):
os.mkdir(test_path)
ptc_params = """
parameters: [l,b,d,mul,mub,vr]
missing_dims: [l,b,d,mul,mub,vr]
"""
sat_params = """
parameters: [l,b,d,mul,mub,vr]
missing_dims: [l,b,d,mul,mub,vr]
"""
_config = minimum_config.format(potential_params="",
particles_params=ptc_params,
satellite_params=sat_params)
config = io.read_config(_config)
model = si.StreamModel.from_config(config)
model.sample_priors()
ix = -3
truth = model.truths[ix]
vals = np.linspace(-0.02, 0., Nfine)
#vals = np.linspace(-0.012,-0.003,Nfine)
Ls = []
for val in vals:
p = model.truths.copy()
p[ix] = val
Ls.append(model(p))
Ls = np.array(Ls)
fig,ax = plt.subplots(1,1,figsize=(8,8))
ax.plot(vals,Ls,marker=None,linestyle='-')
ax.axvline(truth)
fig.savefig(os.path.join(test_path, "{}.png".format("mul")))
fig,ax = plt.subplots(1,1,figsize=(8,8))
ax.plot(vals,np.exp(Ls-np.max(Ls)),marker=None,linestyle='-')
ax.axvline(truth)
fig.savefig(os.path.join(test_path, "{}_exp.png".format("mul")))
def exp1_posterior():
cfg_filename = os.path.join(streamspath, "config", "exp1_8.yml")
config = read_config(cfg_filename)
model = StreamModel.from_config(config)
hdf5_filename = os.path.join(streamspath, "plots", "yeti", "exper1_8", "cache",
"combined_inference.hdf5")
print(hdf5_filename)
if not os.path.exists(hdf5_filename): raise IOError("Path doesn't exist!")
with h5py.File(hdf5_filename, "r") as f:
chain = f["chain"].value
_flatchain = np.vstack(chain)
flatchain = np.zeros_like(_flatchain)
params = OrderedDict(model.parameters['potential'].items() + \
model.parameters['satellite'].items())
truths = []
bounds = []
for ii,p in enumerate(params.values()):
if p.name == 'alpha':
truths.append(np.nan)
bounds.append((1., 2.0))
flatchain[:,ii] = _unit_transform[p.name](_flatchain[:,ii])
continue
truth = _unit_transform[p.name](p.truth)
print(p.name, truth)
truths.append(truth)
bounds.append((0.95*truth, 1.05*truth))
flatchain[:,ii] = _unit_transform[p.name](_flatchain[:,ii])
# bounds = [(0.7,2.),(0.7,2.),(52,142),(100,200),(5,30),(1.1,2.5)]
#bounds = None
fig = triangle.corner(flatchain, plot_datapoints=False,
truths=truths, extents=potential_bounds, labels=potential_labels)
fig.subplots_adjust(wspace=0.13, hspace=0.13)
fig.savefig(os.path.join(plot_path, "exp1_posterior.{}".format(ext)))
def setup(self):
config = io.read_config(_config)
self.model = si.StreamModel.from_config(config)
self.model.sample_priors()
p = model.truths.copy()
p[ix] = val
Ls.append(model(p))
Ls = np.array(Ls)
fig,ax = plt.subplots(1,1,figsize=(8,8))
ax.plot(vals,Ls,marker=None,linestyle='-')
ax.axvline(truth)
fig.savefig(os.path.join(test_path, "{}.png".format("mul")))
fig,ax = plt.subplots(1,1,figsize=(8,8))
ax.plot(vals,np.exp(Ls-np.max(Ls)),marker=None,linestyle='-')
ax.axvline(truth)
fig.savefig(os.path.join(test_path, "{}_exp.png".format("mul")))
if __name__ == "__main__":
import cProfile
import pstats
c = io.read_config(lm10_c)
model = si.StreamModel.from_config(c)
potential = model._potential_class(**model._given_potential_params)
cProfile.run('time_likelihood(model, potential)', 'likelihood_stats')
p = pstats.Stats('likelihood_stats')
p.strip_dirs().sort_stats('cumulative').print_stats(25)
cProfile.run('time_posterior(model)', 'posterior_stats')
p = pstats.Stats('posterior_stats')
p.strip_dirs().sort_stats('cumulative').print_stats(25)
times.append(time.time()-a)
print(np.min(times), "seconds per likelihood call")
_config = """
name: test
data_file: data/observed_particles/2.5e8.hdf5
nparticles: {}
potential:
class_name: LawMajewski2010
parameters: [q1, qz, phi, v_halo]
particles:
parameters: [d,mul,mub,vr]
satellite:
parameters: [d,mul,mub,vr]
""".format(nparticles)
config = io.read_config(_config)
model = si.StreamModel.from_config(config)
truths = model.truths
times = []
for ii in range(10):
a = time.time()
model(truths)
times.append(time.time()-a)
print(np.min(times), "seconds per model call")
times.append(time.time() - a)
print(np.min(times), "seconds per likelihood call")
_config = """
name: test
data_file: data/observed_particles/2.5e8.hdf5
nparticles: {}
potential:
class_name: LawMajewski2010
parameters: [q1, qz, phi, v_halo]
particles:
parameters: [d,mul,mub,vr]
satellite:
parameters: [d,mul,mub,vr]
""".format(nparticles)
config = io.read_config(_config)
model = si.StreamModel.from_config(config)
truths = model.truths
times = []
for ii in range(10):
a = time.time()
model(truths)
times.append(time.time() - a)
print(np.min(times), "seconds per model call")
def simulated_streams():
filename = os.path.join(plot_path, "simulated_streams.{}".format(ext))
fig,axes = plt.subplots(2,4,figsize=grid_figsize,
sharex=True, sharey=True)
ticks = [-100,-50,0,50]
alphas = [0.2, 0.27, 0.34, 0.4]
rcparams = {'lines.linestyle' : 'none',
'lines.marker' : ','}
with rc_context(rc=rcparams):
for ii,_m in enumerate(range(6,9+1)):
alpha = alphas[ii]
mass = "2.5e{}".format(_m)
print(mass)
m = float(mass)
data_filename = os.path.join(streamspath, "data", "observed_particles",
"2.5e{}.hdf5".format(_m))
cfg_filename = os.path.join(streamspath, "config", "exp2.yml".format(_m))
data = read_hdf5(data_filename)
true_particles = data["true_particles"].to_frame(galactocentric)
config = read_config(cfg_filename)
idx = config['particle_idx']
sgr = SgrSimulation(sgr_path.format(_m),snapfile)
p = sgr.particles()
p_bound = sgr.particles(expr="tub==0")
axes[0,ii].text(0.5, 1.05, r"$2.5\times10^{}M_\odot$".format(_m),
horizontalalignment='center',
fontsize=24,
transform=axes[0,ii].transAxes)
axes[0,ii].plot(p["x"].value, p["y"].value,
alpha=alpha, rasterized=True, color='#555555')
axes[1,ii].plot(p["x"].value, p["z"].value,
alpha=alpha, rasterized=True, color='#555555')
if _m == 8:
axes[0,ii].plot(true_particles["x"].value[idx],
true_particles["y"].value[idx],
marker='+', markeredgewidth=1.5,
markersize=8, alpha=0.9, color='k')
axes[1,ii].plot(true_particles["x"].value[idx],
true_particles["z"].value[idx],
marker='+', markeredgewidth=1.5,
markersize=8, alpha=0.9, color='k')
axes[1,ii].set_xticks(ticks)
axes[1,ii].set_xlabel("$X$ [kpc]")
axes[0,0].set_ylabel("$Y$ [kpc]")
axes[1,0].set_ylabel("$Z$ [kpc]")
axes[0,0].set_yticks(ticks)
axes[1,0].set_yticks(ticks)
axes[-1,-1].set_xlim(-110,75)
axes[-1,-1].set_ylim(-110,75)
fig.tight_layout()
fig.subplots_adjust(top=0.92, hspace=0.025, wspace=0.1)
fig.savefig(filename, dpi=200)
p[ix] = val
Ls.append(model(p))
Ls = np.array(Ls)
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
ax.plot(vals, Ls, marker=None, linestyle='-')
ax.axvline(truth)
fig.savefig(os.path.join(test_path, "{}.png".format("mul")))
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
ax.plot(vals, np.exp(Ls - np.max(Ls)), marker=None, linestyle='-')
ax.axvline(truth)
fig.savefig(os.path.join(test_path, "{}_exp.png".format("mul")))
if __name__ == "__main__":
import cProfile
import pstats
c = io.read_config(lm10_c)
model = si.StreamModel.from_config(c)
potential = model._potential_class(**model._given_potential_params)
cProfile.run('time_likelihood(model, potential)', 'likelihood_stats')
p = pstats.Stats('likelihood_stats')
p.strip_dirs().sort_stats('cumulative').print_stats(25)
cProfile.run('time_posterior(model)', 'posterior_stats')
p = pstats.Stats('posterior_stats')
p.strip_dirs().sort_stats('cumulative').print_stats(25)
def trace_plots():
cfg_filename = os.path.join(streamspath, "config", "exp1_8.yml")
config = read_config(cfg_filename)
model = StreamModel.from_config(config)
hdf5_filename = os.path.join(streamspath, "plots", "yeti", "exper1_8", "cache", "combined_inference_all.hdf5")
if not os.path.exists(hdf5_filename): raise IOError("Path doesn't exist!")
print(hdf5_filename)
with h5py.File(hdf5_filename, "r") as f:
chain = f["chain"].value
acor = f["acor"].value
labels = ["$q_1$", "$q_z$", r"$\phi$", "$v_h$", "$r_h$", r"$\alpha$"]
bounds = [(1.2,1.5),(1.2,1.5),(80,110),(111,131),(5,20),(0.5,2.5)]
ticks = [(1.25,1.35,1.45),(1.25,1.35,1.45),(85,95,105),(115,120,125),(7,12,17),(1.,1.5,2.)]
# plot individual walkers
fig,axes = plt.subplots(6,1,figsize=(8.5,11),sharex=True)
k = 0
for gname,group in model.parameters.items():
for pname,p in group.items():
thischain = _unit_transform[pname](chain[...,k])
for ii in range(config['walkers']):
axes.flat[k].plot(thischain[ii,:],
alpha=0.1, marker=None,
drawstyle='steps', color='k', zorder=0)
#axes.flat[k].set_ylabel(labels[k], rotation='horizontal')
axes[k].text(-0.02, 0.5, labels[k],
horizontalalignment='right',
fontsize=22,
transform=axes[k].transAxes)
if pname == "phi":
axes[k].text(1.07, 0.475, "deg",
horizontalalignment='left',
fontsize=18,
transform=axes[k].transAxes)
elif pname == "v_halo":
axes[k].text(1.07, 0.475, "km/s",
horizontalalignment='left',
fontsize=18,
transform=axes[k].transAxes)
elif pname == "log_R_halo":
axes[k].text(1.07, 0.475, "kpc",
horizontalalignment='left',
fontsize=18,
transform=axes[k].transAxes)
axes[k].text(0.25, 0.1, r"$t_{\rm acor}$=" + "{}".format(int(acor[k])),
horizontalalignment='right',
fontsize=18,
transform=axes[k].transAxes)
axes.flat[k].set_yticks(ticks[k])
axes.flat[k].set_xlim(0,10000)
axes.flat[k].set_ylim(bounds[k])
axes.flat[k].yaxis.tick_right()
#axes.flat[k].yaxis.set_label_position("right")
axes.flat[k].set_rasterization_zorder(1)
k += 1
axes.flat[-1].set_xlabel("Step number")
fig.tight_layout()
fig.subplots_adjust(hspace=0.04, left=0.14, right=0.86)
fig.savefig(os.path.join(plot_path, "mcmc_trace.{}".format(ext)))
def main(config_file, mpi=False, threads=None, overwrite=False, continue_sampler=False):
""" TODO: """
# get a pool object given the configuration parameters
# -- This needs to go here so I don't read in the particle file for each thread. --
pool = get_pool(mpi=mpi, threads=threads)
# read configuration from a YAML file
config = io.read_config(config_file)
np.random.seed(config["seed"])
random.seed(config["seed"])
if not os.path.exists(config['streams_path']):
raise IOError("Specified streams path '{}' doesn't exist!".format(config['streams_path']))
logger.debug("Path to streams project: {}".format(config['streams_path']))
# the path to write things to
output_path = config["output_path"]
logger.debug("Will write data to:\n\t{}".format(output_path))
cache_output_path = os.path.join(output_path, "cache")
# get a StreamModel from a config dict
model = si.StreamModel.from_config(config)
logger.info("Model has {} parameters".format(model.nparameters))
if os.path.exists(cache_output_path) and overwrite:
logger.info("Writing over output path '{}'".format(cache_output_path))
logger.debug("Deleting files: '{}'".format(os.listdir(cache_output_path)))
shutil.rmtree(cache_output_path)
# emcee parameters
# read in the number of walkers to use
nwalkers = config["walkers"]
nsteps = config["steps"]
output_every = config.get("output_every", None)
nburn = config.get("burn_in", 0)
start_truth = config.get("start_truth", False)
a = config.get("a", 2.) # emcee tuning param
if not os.path.exists(cache_output_path) and not continue_sampler:
logger.info("Output path '{}' doesn't exist, running inference..."\
.format(cache_output_path))
os.mkdir(cache_output_path)
# sample starting positions
p0 = model.sample_priors(size=nwalkers,
start_truth=start_truth)
logger.debug("Priors sampled...")
if nburn > 0:
sampler = si.StreamModelSampler(model, nwalkers, pool=pool, a=a)
time0 = time.time()
logger.info("Burning in sampler for {} steps...".format(nburn))
pos, xx, yy = sampler.run_mcmc(p0, nburn)
pos = fix_whack_walkers(pos, sampler.acceptance_fraction,
sampler.flatlnprobability, sampler.flatchain,
threshold=config.get("acceptance_threshold", None))
t = time.time() - time0
logger.debug("Spent {} seconds on burn-in...".format(t))
else:
pos = p0
if nsteps > 0:
sampler = si.StreamModelSampler(model, nwalkers, pool=pool, a=a)
sampler.run_inference(pos, nsteps, path=cache_output_path, first_step=0,
output_every=output_every,
output_file_fmt="inference_{:06d}.hdf5")
elif os.path.exists(cache_output_path) and not continue_sampler:
logger.info("Output path '{}' already exists, not running sampler..."\
.format(cache_output_path))
elif os.path.exists(cache_output_path) and continue_sampler:
if len(os.listdir(cache_output_path)) == 0:
logger.error("No files in path: {}".format(cache_output_path))
sys.exit(1)
continue_files = glob.glob(os.path.join(cache_output_path, "inference_*.hdf5"))
continue_file = config.get("continue_file", sorted(continue_files)[-1])
continue_file = os.path.join(cache_output_path, continue_file)
if not os.path.exists(continue_file):
logger.error("File {} doesn't exist!".format(continue_file))
sys.exit(1)
with h5py.File(continue_file, "r") as f:
old_chain = f["chain"].value
old_flatchain = np.vstack(old_chain)
old_lnprobability = f["lnprobability"].value
old_flatlnprobability = np.vstack(old_lnprobability)
old_acc_frac = f["acceptance_fraction"].value
last_step = f["last_step"].value
pos = old_chain[:,-1]
pos = fix_whack_walkers(pos, old_acc_frac,
old_flatlnprobability,
old_flatchain,
threshold=config.get("acceptance_threshold", None))
sampler = si.StreamModelSampler(model, nwalkers, pool=pool, a=a)
logger.info("Continuing sampler...running {} walkers for {} steps..."\
.format(nwalkers, nsteps))
sampler.run_inference(pos, nsteps, path=cache_output_path, first_step=last_step,
output_every=output_every,
output_file_fmt = "inference_{:07d}.hdf5")
else:
print("Unknown state.")
sys.exit(1)
pool.close() if hasattr(pool, 'close') else None
#############################################################
# Plotting
#
plot_config = config.get("plot", dict())
plot_ext = plot_config.get("ext", "png")
# glob properly orders the list
for filename in sorted(glob.glob(os.path.join(cache_output_path,"inference_*.hdf5"))):
logger.debug("Reading file {}...".format(filename))
with h5py.File(filename, "r") as f:
try:
chain = np.hstack((chain,f["chain"].value))
except NameError:
chain = f["chain"].value
acceptance_fraction = f["acceptance_fraction"].value
try:
acor = autocorr.integrated_time(np.mean(chain, axis=0), axis=0,
window=50) # 50 comes from emcee
except:
acor = []
flatchain = np.vstack(chain)
# thin chain
if config.get("thin_chain", True):
if len(acor) > 0:
t_med = np.median(acor)
thin_chain = chain[:,::int(t_med)]
thin_flatchain = np.vstack(thin_chain)
logger.info("Median autocorrelation time: {}".format(t_med))
else:
logger.warn("FAILED TO THIN CHAIN")
thin_chain = chain
thin_flatchain = flatchain
else:
thin_chain = chain
thin_flatchain = flatchain
# plot true_particles, true_satellite over the rest of the stream
gc_particles = model.true_particles.to_frame(galactocentric)
m = model.true_satellite.mass
# HACK
sgr = SgrSimulation("sgr_nfw/M2.5e+0{}".format(int(np.floor(np.log10(m)))), "SNAP113")
all_gc_particles = sgr.particles(n=1000, expr="tub!=0").to_frame(galactocentric)
fig,axes = plt.subplots(1,2,figsize=(16,8))
axes[0].plot(all_gc_particles["x"].value, all_gc_particles["z"].value,
markersize=10., marker='.', linestyle='none', alpha=0.25)
axes[0].plot(gc_particles["x"].value, gc_particles["z"].value,
markersize=10., marker='o', linestyle='none', alpha=0.75)
axes[1].plot(all_gc_particles["vx"].to(u.km/u.s).value,
all_gc_particles["vz"].to(u.km/u.s).value,
markersize=10., marker='.', linestyle='none', alpha=0.25)
axes[1].plot(gc_particles["vx"].to(u.km/u.s).value,
gc_particles["vz"].to(u.km/u.s).value,
markersize=10., marker='o', linestyle='none', alpha=0.75)
fig.savefig(os.path.join(output_path, "xyz_vxvyvz.{}".format(plot_ext)))
if plot_config.get("mcmc_diagnostics", False):
logger.debug("Plotting MCMC diagnostics...")
diagnostics_path = os.path.join(output_path, "diagnostics")
if not os.path.exists(diagnostics_path):
os.mkdir(diagnostics_path)
# plot histogram of autocorrelation times
if len(acor) > 0:
fig,ax = plt.subplots(1,1,figsize=(12,6))
ax.plot(acor, marker='o', linestyle='none') #model.nparameters//5)
ax.set_xlabel("Parameter index")
ax.set_ylabel("Autocorrelation time")
fig.savefig(os.path.join(diagnostics_path, "acor.{}".format(plot_ext)))
# plot histogram of acceptance fractions
fig,ax = plt.subplots(1,1,figsize=(8,8))
ax.hist(acceptance_fraction, bins=nwalkers//5)
ax.set_xlabel("Acceptance fraction")
fig.suptitle("Histogram of acceptance fractions for all walkers")
fig.savefig(os.path.join(diagnostics_path, "acc_frac.{}".format(plot_ext)))
# plot individual walkers
plt.figure(figsize=(12,6))
for k in range(model.nparameters):
plt.clf()
for ii in range(nwalkers):
plt.plot(chain[ii,:,k], alpha=0.4, drawstyle='steps', color='k')
plt.axhline(model.truths[k], color='r', lw=2., linestyle='-', alpha=0.5)
plt.savefig(os.path.join(diagnostics_path, "param_{}.{}".format(k, plot_ext)))
plt.close('all')
if plot_config.get("posterior", False):
logger.debug("Plotting posterior distributions...")
flatchain_dict = model.label_flatchain(thin_flatchain)
p0 = model.sample_priors(size=1000) # HACK HACK HACK
p0_dict = model.label_flatchain(np.vstack(p0))
potential_group = model.parameters.get('potential', None)
particles_group = model.parameters.get('particles', None)
satellite_group = model.parameters.get('satellite', None)
flatchains = dict()
if potential_group:
this_flatchain = np.zeros((len(thin_flatchain),len(potential_group)))
this_p0 = np.zeros((len(p0),len(potential_group)))
this_truths = []
this_extents = []
for ii,pname in enumerate(potential_group.keys()):
f = _unit_transform[pname]
p = model.parameters['potential'][pname]
this_flatchain[:,ii] = f(np.squeeze(flatchain_dict['potential'][pname]))
this_p0[:,ii] = f(np.squeeze(p0_dict['potential'][pname]))
this_truths.append(f(p.truth))
this_extents.append((f(p._prior.a), f(p._prior.b)))
print(pname, np.median(this_flatchain[:,ii]), np.std(this_flatchain[:,ii]))
fig = triangle.corner(this_p0,
point_kwargs=dict(color='#2b8cbe',alpha=0.1),
hist_kwargs=dict(color='#2b8cbe',alpha=0.75,normed=True,bins=50),
plot_contours=False)
fig = triangle.corner(this_flatchain,
fig=fig,
truths=this_truths,
labels=[_label_map[k] for k in potential_group.keys()],
extents=this_extents,
point_kwargs=dict(color='k',alpha=1.),
hist_kwargs=dict(color='k',alpha=0.75,normed=True,bins=50))
fig.savefig(os.path.join(output_path, "potential.{}".format(plot_ext)))
flatchains['potential'] = this_flatchain
nparticles = model.true_particles.nparticles
if particles_group and len(particles_group) > 1:
for jj in range(nparticles):
this_flatchain = np.zeros((len(thin_flatchain),len(particles_group)))
this_p0 = np.zeros((len(p0),len(particles_group)))
this_truths = []
this_extents = None
for ii,pname in enumerate(particles_group.keys()):
f = _unit_transform[pname]
p = model.parameters['particles'][pname]
this_flatchain[:,ii] = f(np.squeeze(flatchain_dict['particles'][pname][:,jj]))
this_p0[:,ii] = f(np.squeeze(p0_dict['particles'][pname][:,jj]))
this_truths.append(f(p.truth[jj]))
#this_extents.append((f(p._prior.a), f(p._prior.b)))
fig = triangle.corner(this_p0,
point_kwargs=dict(color='#2b8cbe',alpha=0.1),
hist_kwargs=dict(color='#2b8cbe',alpha=0.75,normed=True,bins=50),
plot_contours=False)
fig = triangle.corner(this_flatchain,
fig=fig,
truths=this_truths,
labels=[_label_map[k] for k in particles_group.keys()],
extents=this_extents,
point_kwargs=dict(color='k',alpha=1.),
hist_kwargs=dict(color='k',alpha=0.75,normed=True,bins=50))
fig.savefig(os.path.join(output_path, "particle{}.{}".format(jj,plot_ext)))
# plot the posterior for the satellite parameters
if satellite_group and len(satellite_group) > 1:
jj = 0
this_flatchain = np.zeros((len(thin_flatchain),len(satellite_group)))
this_p0 = np.zeros((len(p0),len(satellite_group)))
this_truths = []
this_extents = None
for ii,pname in enumerate(satellite_group.keys()):
f = _unit_transform[pname]
p = model.parameters['satellite'][pname]
this_flatchain[:,ii] = f(np.squeeze(flatchain_dict['satellite'][pname][:,jj]))
this_p0[:,ii] = f(np.squeeze(p0_dict['satellite'][pname][:,jj]))
try:
this_truths.append(f(p.truth[jj]))
except: # IndexError:
this_truths.append(f(p.truth))
#this_extents.append((f(p._prior.a), f(p._prior.b)))
fig = triangle.corner(this_p0,
point_kwargs=dict(color='#2b8cbe',alpha=0.1),
hist_kwargs=dict(color='#2b8cbe',alpha=0.75,normed=True,bins=50),
plot_contours=False)
fig = triangle.corner(this_flatchain,
fig=fig,
truths=this_truths,
labels=[_label_map[k] for k in satellite_group.keys()],
extents=this_extents,
point_kwargs=dict(color='k',alpha=1.),
hist_kwargs=dict(color='k',alpha=0.75,normed=True,bins=50))
fig.savefig(os.path.join(output_path, "satellite.{}".format(plot_ext)))
flatchains['satellite'] = this_flatchain
if flatchains.has_key('potential') and flatchains.has_key('satellite'):
this_flatchain = np.hstack((flatchains['potential'],flatchains['satellite']))
labels = [_label_map[k] for k in potential_group.keys()+satellite_group.keys()]
fig = triangle.corner(this_flatchain,
labels=labels,
point_kwargs=dict(color='k',alpha=1.),
hist_kwargs=dict(color='k',alpha=0.75,normed=True,bins=50))
fig.savefig(os.path.join(output_path, "suck-it-up.{}".format(plot_ext)))
def test_per_particle(self):
_c = minimum_config.format(potential_params=pot_params,
particles_params="",
satellite_params=sat_params)
config = io.read_config(_c)
model = si.StreamModel.from_config(config)
model.sample_priors()
test_path = os.path.join(output_path, "model")
if not os.path.exists(test_path):
os.mkdir(test_path)
# likelihood args
t1, t2, dt = model.lnpargs
p_gc = model.true_particles.to_frame(galactocentric)._X
s_gc = model.true_satellite.to_frame(galactocentric)._X
logmass = model.satellite.logmass.truth
logmdot = model.satellite.logmdot.truth
#true_alpha = model.satellite.alpha.truth
true_alpha = 1.4
beta = model.particles.beta.truth
tub = model.particles.tub.truth
truth_dict = model._decompose_vector(model.truths)
group = truth_dict['potential']
for param_name, truths in group.items():
print(param_name)
param = model.parameters['potential'][param_name]
vals = np.linspace(0.9, 1.1, Nfine) * truths
pparams = dict()
Ls = []
for val in vals:
pparams[param_name] = val
potential = model._potential_class(**pparams)
ln_like = back_integration_likelihood(t1, t2, dt, potential,
p_gc, s_gc, logmass,
logmdot, beta,
true_alpha, tub)
Ls.append(ln_like)
Ls = np.array(Ls).T
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
for ii, Lvec in enumerate(Ls):
ax.plot(vals,
Lvec,
marker=None,
linestyle='-',
label=str(ii),
alpha=0.5)
if param_name == "v_halo":
ax.set_ylim(-300, 50)
ax.axvline(truths)
ax.legend(loc='lower right', fontsize=14)
fig.savefig(
os.path.join(test_path,
"per_particle_{}.png".format(param_name)))
#########################
# alpha
param = model.parameters['satellite']['alpha']
vals = np.linspace(0.5, 2.5, Nfine)
potential = model._potential_class()
Ls = []
for val in vals:
ln_like = back_integration_likelihood(t1, t2, dt, potential, p_gc,
s_gc, logmass, logmdot, beta,
val, tub)
Ls.append(ln_like)
Ls = np.array(Ls).T
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
for ii, Lvec in enumerate(Ls):
ax.plot(vals,
Lvec,
marker=None,
linestyle='-',
label=str(ii),
alpha=0.5)
ax.axvline(true_alpha)
ax.legend(loc='lower right', fontsize=14)
fig.savefig(os.path.join(test_path, "per_particle_alpha.png"))
plt.close('all')
def setup(self):
config = io.read_config(_config)
self.model = si.StreamModel.from_config(config)
self.model.sample_priors()
def test_per_particle(self):
_c = minimum_config.format(potential_params=pot_params,
particles_params="",
satellite_params=sat_params)
config = io.read_config(_c)
model = si.StreamModel.from_config(config)
model.sample_priors()
test_path = os.path.join(output_path, "model")
if not os.path.exists(test_path):
os.mkdir(test_path)
# likelihood args
t1, t2, dt = model.lnpargs
p_gc = model.true_particles.to_frame(galactocentric)._X
s_gc = model.true_satellite.to_frame(galactocentric)._X
logmass = model.satellite.logmass.truth
logmdot = model.satellite.logmdot.truth
#true_alpha = model.satellite.alpha.truth
true_alpha = 1.4
beta = model.particles.beta.truth
tub = model.particles.tub.truth
truth_dict = model._decompose_vector(model.truths)
group = truth_dict['potential']
for param_name,truths in group.items():
print(param_name)
param = model.parameters['potential'][param_name]
vals = np.linspace(0.9,1.1,Nfine)*truths
pparams = dict()
Ls = []
for val in vals:
pparams[param_name] = val
potential = model._potential_class(**pparams)
ln_like = back_integration_likelihood(t1, t2, dt,
potential, p_gc, s_gc,
logmass, logmdot,
beta, true_alpha, tub)
Ls.append(ln_like)
Ls = np.array(Ls).T
fig,ax = plt.subplots(1,1,figsize=(8,8))
for ii,Lvec in enumerate(Ls):
ax.plot(vals,Lvec,marker=None,linestyle='-',
label=str(ii), alpha=0.5)
if param_name == "v_halo":
ax.set_ylim(-300,50)
ax.axvline(truths)
ax.legend(loc='lower right', fontsize=14)
fig.savefig(os.path.join(test_path, "per_particle_{}.png".format(param_name)))
#########################
# alpha
param = model.parameters['satellite']['alpha']
vals = np.linspace(0.5,2.5,Nfine)
potential = model._potential_class()
Ls = []
for val in vals:
ln_like = back_integration_likelihood(t1, t2, dt,
potential, p_gc, s_gc,
logmass, logmdot,
beta, val, tub)
Ls.append(ln_like)
Ls = np.array(Ls).T
fig,ax = plt.subplots(1,1,figsize=(8,8))
for ii,Lvec in enumerate(Ls):
ax.plot(vals,Lvec,marker=None,linestyle='-',
label=str(ii), alpha=0.5)
ax.axvline(true_alpha)
ax.legend(loc='lower right', fontsize=14)
fig.savefig(os.path.join(test_path, "per_particle_alpha.png"))
plt.close('all')
def exp_posteriors(exp_num):
matplotlib.rc('xtick', labelsize=16)
matplotlib.rc('ytick', labelsize=16)
cfg_filename = os.path.join(streamspath, "config", "exp{}.yml".format(exp_num))
config = read_config(cfg_filename)
model = StreamModel.from_config(config)
cache_path = os.path.join(streamspath, "plots", "yeti",
"exper{}_marg_tub".format(exp_num), "cache")
filename = os.path.join(cache_path, "combined_inference.hdf5")
with h5py.File(filename, "r") as f:
chain = f["chain"].value
_flatchain = np.vstack(chain)
d = model.label_flatchain(_flatchain)
# Potential
this_flatchain = np.zeros((_flatchain.shape[0], len(d["potential"])))
truths = []
labels = []
for ii,pname in enumerate(d["potential"].keys()):
this_flatchain[:,ii] = _unit_transform[pname](np.squeeze(d["potential"][pname]))
p = model.parameters["potential"][pname]
truth = _unit_transform[pname](p.truth)
truths.append(truth)
labels.append(_label_map[pname])
q16,q50,q84 = np.array(np.percentile(this_flatchain, [16, 50, 84], axis=0))
q_m, q_p = q50-q16, q84-q50
for ii,pname in enumerate(d["potential"].keys()):
print("{} \n\t truth={:.2f}\n\t measured={:.2f}+{:.2f}-{:.2f}"\
.format(pname,truths[ii],q50[ii],q_p[ii],q_m[ii]))
fig = triangle.corner(this_flatchain, plot_datapoints=False,
truths=truths, extents=potential_bounds, labels=potential_labels)
fig.subplots_adjust(wspace=0.13, hspace=0.13)
fig.savefig(os.path.join(plot_path, "exp{}_potential.{}".format(exp_num, ext)))
# Particle
p_idx = 2
this_flatchain = np.zeros((_flatchain.shape[0], len(d["particles"])))
truths = []
bounds = []
labels = []
for ii,pname in enumerate(d["particles"].keys()):
this_flatchain[:,ii] = _unit_transform[pname](d["particles"][pname][:,p_idx])
p = model.parameters["particles"][pname]
truth = _unit_transform[pname](p.truth[p_idx])
truths.append(truth)
if pname == "tub":
bounds.append((model.lnpargs[1], model.lnpargs[0]))
else:
sig = model.particles.errors[pname].value[p_idx]
mu = model.particles[pname].value[p_idx]
bounds.append((mu-3*sig, mu+3*sig))
labels.append(_label_map[pname])
q16,q50,q84 = np.array(np.percentile(this_flatchain, [16, 50, 84], axis=0))
q_m, q_p = q50-q16, q84-q50
for ii,pname in enumerate(d["particles"].keys()):
print("{} \n\t truth={:.2f}\n\t measured={:.2f}+{:.2f}-{:.2f}"\
.format(pname,truths[ii],q50[ii],q_p[ii],q_m[ii]))
# HACK
bounds = [(20.,29.), (-9.5, -7.), (0.,2.), (-55,-5)]
# OLD: bounds = [(22.,26.), (-8.6, -8.), (1.0,1.5), (-50,-10)]
# bounds = None
fig = triangle.corner(this_flatchain, plot_datapoints=False,
truths=truths, labels=labels, extents=bounds)
fig.subplots_adjust(wspace=0.13, hspace=0.13)
fig.savefig(os.path.join(plot_path, "exp{}_particle.{}".format(exp_num, ext)))
# Satellite
this_flatchain = np.zeros((_flatchain.shape[0], len(d["satellite"])))
truths = []
bounds = []
labels = []
#for ii,pname in enumerate(keys):
for ii,pname in enumerate(d["satellite"].keys()):
this_flatchain[:,ii] = _unit_transform[pname](d["satellite"][pname][:,0])
p = model.parameters["satellite"][pname]
truth = _unit_transform[pname](p.truth)
if pname == "alpha":
bounds.append((1., 2.5))
truths.append(np.nan)
else:
truths.append(truth)
sig = model.satellite.errors[pname].value[0]
mu = model.satellite[pname].value[0]
bounds.append((mu-3*sig, mu+3*sig))
labels.append(_label_map[pname])
# HACK
bounds = [(28.5,33.), (-2.6,-1.5), (1.3,2.0), (120,175), bounds[-1]]
# bounds = None
if len(d["satellite"]) > len(bounds):
bounds = [(0,10), (-20,5)] + bounds
#bounds = None
fig = triangle.corner(this_flatchain, plot_datapoints=False,
truths=truths, labels=labels, extents=bounds)
fig.subplots_adjust(wspace=0.13, hspace=0.13)
fig.savefig(os.path.join(plot_path, "exp{}_satellite.{}".format(exp_num, ext)))
def main(config_file,
mpi=False,
threads=None,
overwrite=False,
continue_sampler=False):
""" TODO: """
# get a pool object given the configuration parameters
# -- This needs to go here so I don't read in the particle file for each thread. --
pool = get_pool(mpi=mpi, threads=threads)
# read configuration from a YAML file
config = io.read_config(config_file)
np.random.seed(config["seed"])
random.seed(config["seed"])
if not os.path.exists(config['streams_path']):
raise IOError("Specified streams path '{}' doesn't exist!".format(
config['streams_path']))
logger.debug("Path to streams project: {}".format(config['streams_path']))
# the path to write things to
output_path = config["output_path"]
logger.debug("Will write data to:\n\t{}".format(output_path))
cache_output_path = os.path.join(output_path, "cache")
# get a StreamModel from a config dict
model = si.StreamModel.from_config(config)
logger.info("Model has {} parameters".format(model.nparameters))
if os.path.exists(cache_output_path) and overwrite:
logger.info("Writing over output path '{}'".format(cache_output_path))
logger.debug("Deleting files: '{}'".format(
os.listdir(cache_output_path)))
shutil.rmtree(cache_output_path)
# emcee parameters
# read in the number of walkers to use
nwalkers = config["walkers"]
nsteps = config["steps"]
output_every = config.get("output_every", None)
nburn = config.get("burn_in", 0)
start_truth = config.get("start_truth", False)
a = config.get("a", 2.) # emcee tuning param
if not os.path.exists(cache_output_path) and not continue_sampler:
logger.info("Output path '{}' doesn't exist, running inference..."\
.format(cache_output_path))
os.mkdir(cache_output_path)
# sample starting positions
p0 = model.sample_priors(size=nwalkers, start_truth=start_truth)
logger.debug("Priors sampled...")
if nburn > 0:
sampler = si.StreamModelSampler(model, nwalkers, pool=pool, a=a)
time0 = time.time()
logger.info("Burning in sampler for {} steps...".format(nburn))
pos, xx, yy = sampler.run_mcmc(p0, nburn)
pos = fix_whack_walkers(pos,
sampler.acceptance_fraction,
sampler.flatlnprobability,
sampler.flatchain,
threshold=config.get(
"acceptance_threshold", None))
t = time.time() - time0
logger.debug("Spent {} seconds on burn-in...".format(t))
else:
pos = p0
if nsteps > 0:
sampler = si.StreamModelSampler(model, nwalkers, pool=pool, a=a)
sampler.run_inference(pos,
nsteps,
path=cache_output_path,
first_step=0,
output_every=output_every,
output_file_fmt="inference_{:06d}.hdf5")
elif os.path.exists(cache_output_path) and not continue_sampler:
logger.info("Output path '{}' already exists, not running sampler..."\
.format(cache_output_path))
elif os.path.exists(cache_output_path) and continue_sampler:
if len(os.listdir(cache_output_path)) == 0:
logger.error("No files in path: {}".format(cache_output_path))
sys.exit(1)
continue_files = glob.glob(
os.path.join(cache_output_path, "inference_*.hdf5"))
continue_file = config.get("continue_file", sorted(continue_files)[-1])
continue_file = os.path.join(cache_output_path, continue_file)
if not os.path.exists(continue_file):
logger.error("File {} doesn't exist!".format(continue_file))
sys.exit(1)
with h5py.File(continue_file, "r") as f:
old_chain = f["chain"].value
old_flatchain = np.vstack(old_chain)
old_lnprobability = f["lnprobability"].value
old_flatlnprobability = np.vstack(old_lnprobability)
old_acc_frac = f["acceptance_fraction"].value
last_step = f["last_step"].value
pos = old_chain[:, -1]
pos = fix_whack_walkers(pos,
old_acc_frac,
old_flatlnprobability,
old_flatchain,
threshold=config.get("acceptance_threshold",
None))
sampler = si.StreamModelSampler(model, nwalkers, pool=pool, a=a)
logger.info("Continuing sampler...running {} walkers for {} steps..."\
.format(nwalkers, nsteps))
sampler.run_inference(pos,
nsteps,
path=cache_output_path,
first_step=last_step,
output_every=output_every,
output_file_fmt="inference_{:07d}.hdf5")
else:
print("Unknown state.")
sys.exit(1)
pool.close() if hasattr(pool, 'close') else None
#############################################################
# Plotting
#
plot_config = config.get("plot", dict())
plot_ext = plot_config.get("ext", "png")
# glob properly orders the list
for filename in sorted(
glob.glob(os.path.join(cache_output_path, "inference_*.hdf5"))):
logger.debug("Reading file {}...".format(filename))
with h5py.File(filename, "r") as f:
try:
chain = np.hstack((chain, f["chain"].value))
except NameError:
chain = f["chain"].value
acceptance_fraction = f["acceptance_fraction"].value
try:
acor = autocorr.integrated_time(np.mean(chain, axis=0),
axis=0,
window=50) # 50 comes from emcee
except:
acor = []
flatchain = np.vstack(chain)
# thin chain
if config.get("thin_chain", True):
if len(acor) > 0:
t_med = np.median(acor)
thin_chain = chain[:, ::int(t_med)]
thin_flatchain = np.vstack(thin_chain)
logger.info("Median autocorrelation time: {}".format(t_med))
else:
logger.warn("FAILED TO THIN CHAIN")
thin_chain = chain
thin_flatchain = flatchain
else:
thin_chain = chain
thin_flatchain = flatchain
# plot true_particles, true_satellite over the rest of the stream
gc_particles = model.true_particles.to_frame(galactocentric)
m = model.true_satellite.mass
# HACK
sgr = SgrSimulation("sgr_nfw/M2.5e+0{}".format(int(np.floor(np.log10(m)))),
"SNAP113")
all_gc_particles = sgr.particles(n=1000,
expr="tub!=0").to_frame(galactocentric)
fig, axes = plt.subplots(1, 2, figsize=(16, 8))
axes[0].plot(all_gc_particles["x"].value,
all_gc_particles["z"].value,
markersize=10.,
marker='.',
linestyle='none',
alpha=0.25)
axes[0].plot(gc_particles["x"].value,
gc_particles["z"].value,
markersize=10.,
marker='o',
linestyle='none',
alpha=0.75)
axes[1].plot(all_gc_particles["vx"].to(u.km / u.s).value,
all_gc_particles["vz"].to(u.km / u.s).value,
markersize=10.,
marker='.',
linestyle='none',
alpha=0.25)
axes[1].plot(gc_particles["vx"].to(u.km / u.s).value,
gc_particles["vz"].to(u.km / u.s).value,
markersize=10.,
marker='o',
linestyle='none',
alpha=0.75)
fig.savefig(os.path.join(output_path, "xyz_vxvyvz.{}".format(plot_ext)))
if plot_config.get("mcmc_diagnostics", False):
logger.debug("Plotting MCMC diagnostics...")
diagnostics_path = os.path.join(output_path, "diagnostics")
if not os.path.exists(diagnostics_path):
os.mkdir(diagnostics_path)
# plot histogram of autocorrelation times
if len(acor) > 0:
fig, ax = plt.subplots(1, 1, figsize=(12, 6))
ax.plot(acor, marker='o', linestyle='none') #model.nparameters//5)
ax.set_xlabel("Parameter index")
ax.set_ylabel("Autocorrelation time")
fig.savefig(
os.path.join(diagnostics_path, "acor.{}".format(plot_ext)))
# plot histogram of acceptance fractions
fig, ax = plt.subplots(1, 1, figsize=(8, 8))
ax.hist(acceptance_fraction, bins=nwalkers // 5)
ax.set_xlabel("Acceptance fraction")
fig.suptitle("Histogram of acceptance fractions for all walkers")
fig.savefig(
os.path.join(diagnostics_path, "acc_frac.{}".format(plot_ext)))
# plot individual walkers
plt.figure(figsize=(12, 6))
for k in range(model.nparameters):
plt.clf()
for ii in range(nwalkers):
plt.plot(chain[ii, :, k],
alpha=0.4,
drawstyle='steps',
color='k')
plt.axhline(model.truths[k],
color='r',
lw=2.,
linestyle='-',
alpha=0.5)
plt.savefig(
os.path.join(diagnostics_path,
"param_{}.{}".format(k, plot_ext)))
plt.close('all')
if plot_config.get("posterior", False):
logger.debug("Plotting posterior distributions...")
flatchain_dict = model.label_flatchain(thin_flatchain)
p0 = model.sample_priors(size=1000) # HACK HACK HACK
p0_dict = model.label_flatchain(np.vstack(p0))
potential_group = model.parameters.get('potential', None)
particles_group = model.parameters.get('particles', None)
satellite_group = model.parameters.get('satellite', None)
flatchains = dict()
if potential_group:
this_flatchain = np.zeros(
(len(thin_flatchain), len(potential_group)))
this_p0 = np.zeros((len(p0), len(potential_group)))
this_truths = []
this_extents = []
for ii, pname in enumerate(potential_group.keys()):
f = _unit_transform[pname]
p = model.parameters['potential'][pname]
this_flatchain[:, ii] = f(
np.squeeze(flatchain_dict['potential'][pname]))
this_p0[:, ii] = f(np.squeeze(p0_dict['potential'][pname]))
this_truths.append(f(p.truth))
this_extents.append((f(p._prior.a), f(p._prior.b)))
print(pname, np.median(this_flatchain[:, ii]),
np.std(this_flatchain[:, ii]))
fig = triangle.corner(this_p0,
point_kwargs=dict(color='#2b8cbe',
alpha=0.1),
hist_kwargs=dict(color='#2b8cbe',
alpha=0.75,
normed=True,
bins=50),
plot_contours=False)
fig = triangle.corner(
this_flatchain,
fig=fig,
truths=this_truths,
labels=[_label_map[k] for k in potential_group.keys()],
extents=this_extents,
point_kwargs=dict(color='k', alpha=1.),
hist_kwargs=dict(color='k', alpha=0.75, normed=True, bins=50))
fig.savefig(
os.path.join(output_path, "potential.{}".format(plot_ext)))
flatchains['potential'] = this_flatchain
nparticles = model.true_particles.nparticles
if particles_group and len(particles_group) > 1:
for jj in range(nparticles):
this_flatchain = np.zeros(
(len(thin_flatchain), len(particles_group)))
this_p0 = np.zeros((len(p0), len(particles_group)))
this_truths = []
this_extents = None
for ii, pname in enumerate(particles_group.keys()):
f = _unit_transform[pname]
p = model.parameters['particles'][pname]
this_flatchain[:, ii] = f(
np.squeeze(flatchain_dict['particles'][pname][:, jj]))
this_p0[:, ii] = f(
np.squeeze(p0_dict['particles'][pname][:, jj]))
this_truths.append(f(p.truth[jj]))
#this_extents.append((f(p._prior.a), f(p._prior.b)))
fig = triangle.corner(this_p0,
point_kwargs=dict(color='#2b8cbe',
alpha=0.1),
hist_kwargs=dict(color='#2b8cbe',
alpha=0.75,
normed=True,
bins=50),
plot_contours=False)
fig = triangle.corner(
this_flatchain,
fig=fig,
truths=this_truths,
labels=[_label_map[k] for k in particles_group.keys()],
extents=this_extents,
point_kwargs=dict(color='k', alpha=1.),
hist_kwargs=dict(color='k',
alpha=0.75,
normed=True,
bins=50))
fig.savefig(
os.path.join(output_path,
"particle{}.{}".format(jj, plot_ext)))
# plot the posterior for the satellite parameters
if satellite_group and len(satellite_group) > 1:
jj = 0
this_flatchain = np.zeros(
(len(thin_flatchain), len(satellite_group)))
this_p0 = np.zeros((len(p0), len(satellite_group)))
this_truths = []
this_extents = None
for ii, pname in enumerate(satellite_group.keys()):
f = _unit_transform[pname]
p = model.parameters['satellite'][pname]
this_flatchain[:, ii] = f(
np.squeeze(flatchain_dict['satellite'][pname][:, jj]))
this_p0[:,
ii] = f(np.squeeze(p0_dict['satellite'][pname][:, jj]))
try:
this_truths.append(f(p.truth[jj]))
except: # IndexError:
this_truths.append(f(p.truth))
#this_extents.append((f(p._prior.a), f(p._prior.b)))
fig = triangle.corner(this_p0,
point_kwargs=dict(color='#2b8cbe',
alpha=0.1),
hist_kwargs=dict(color='#2b8cbe',
alpha=0.75,
normed=True,
bins=50),
plot_contours=False)
fig = triangle.corner(
this_flatchain,
fig=fig,
truths=this_truths,
labels=[_label_map[k] for k in satellite_group.keys()],
extents=this_extents,
point_kwargs=dict(color='k', alpha=1.),
hist_kwargs=dict(color='k', alpha=0.75, normed=True, bins=50))
fig.savefig(
os.path.join(output_path, "satellite.{}".format(plot_ext)))
flatchains['satellite'] = this_flatchain
if flatchains.has_key('potential') and flatchains.has_key('satellite'):
this_flatchain = np.hstack(
(flatchains['potential'], flatchains['satellite']))
labels = [
_label_map[k]
for k in potential_group.keys() + satellite_group.keys()
]
fig = triangle.corner(this_flatchain,
labels=labels,
point_kwargs=dict(color='k', alpha=1.),
hist_kwargs=dict(color='k',
alpha=0.75,
normed=True,
bins=50))
fig.savefig(
os.path.join(output_path, "suck-it-up.{}".format(plot_ext)))