def fig_rv():
plt.rcParams['lines.markersize'] = 3
post = ktwo19.keplerian.max_a_posteriori()
plotter = orbit_plots.GPMultipanelPlot(
post,
subtract_orbit_model=False,
nobin=True,
phase_nrows=None,
phase_ncols=3,
)
fig = plt.figure(figsize=(8, 5.5))
ax1 = plt.subplot2grid((2, 3), (0, 0), colspan=3)
ax2 = plt.subplot2grid(
(2, 3),
(1, 0),
)
ax3 = plt.subplot2grid(
(2, 3),
(1, 1),
)
ax4 = plt.subplot2grid(
(2, 3),
(1, 2),
)
axL = [ax1, ax2, ax3, ax4]
plt.rc('font', size=9)
plotter.nobin = True
plotter.legend = False
plotter.epoch = 2454833
plotter.phasetext_size = 'small'
plt.sca(ax1)
plotter.plot_timeseries()
radvel.plot.labelfig(97)
plt.sca(ax2)
plotter.plot_phasefold(98, 1)
plt.sca(ax3)
plotter.plot_phasefold(99, 2)
plt.sca(ax4)
plotter.plot_phasefold(100, 3)
plt.setp(axL[2:], ylabel='')
_ = plt.setp(axL[1:],
ylim=(-23, 23),
yticks=[-20, -15, -10, -5, 0, 5, 10, 15, 20])
_ = plt.setp(axL[0], ylim=(-38, 38), xlim=(2200, 3300))
plt.tight_layout(True)
plt.subplots_adjust(wspace=0.2)
def plots(args):
"""
Generate plots
Args:
args (ArgumentParser): command line arguments
"""
config_file = args.setupfn
conf_base = os.path.basename(config_file).split('.')[0]
statfile = os.path.join(
args.outputdir, "{}_radvel.stat".format(conf_base)
)
status = load_status(statfile)
P, post = radvel.utils.initialize_posterior(config_file,
decorr=args.decorr)
assert status.getboolean('fit', 'run'), \
"Must perform max-liklihood fit before plotting"
post = radvel.posterior.load(status.get('fit', 'postfile'))
for ptype in args.type:
print("Creating {} plot for {}".format(ptype, conf_base))
if ptype == 'rv':
args.plotkw['uparams'] = post.uparams
args.plotkw['status'] = status
if 'saveplot' not in args.plotkw:
saveto = os.path.join(
args.outputdir, conf_base+'_rv_multipanel.pdf'
)
else:
saveto = args.plotkw['saveplot']
args.plotkw.pop('saveplot')
P, _ = radvel.utils.initialize_posterior(config_file)
if hasattr(P, 'bjd0'):
args.plotkw['epoch'] = P.bjd0
if args.gp:
GPPlot = orbit_plots.GPMultipanelPlot(
post, saveplot=saveto, **args.plotkw
)
GPPlot.plot_multipanel()
else:
RVPlot = orbit_plots.MultipanelPlot(
post, saveplot=saveto, **args.plotkw
)
RVPlot.plot_multipanel()
# check to make sure that Posterior is not GP, print warning if it is
if isinstance(post.likelihood, radvel.likelihood.CompositeLikelihood):
like_list = post.likelihood.like_list
else:
like_list = [post.likelihood]
for like in like_list:
if isinstance(like, radvel.likelihood.GPLikelihood):
print("WARNING: GP Likelihood(s) detected. \
You may want to use the '--gp' flag when making these plots.")
break
if ptype == 'corner' or ptype == 'auto' or ptype == 'trend':
assert status.getboolean('mcmc', 'run'), \
"Must run MCMC before making corner, auto, or trend plots"
chains = pd.read_csv(status.get('mcmc', 'chainfile'))
autocorr = pd.read_csv(status.get('mcmc', 'autocorrfile'))
if ptype == 'auto':
saveto = os.path.join(args.outputdir, conf_base+'_auto.pdf')
Auto = mcmc_plots.AutoPlot(autocorr, saveplot=saveto)
Auto.plot()
if ptype == 'corner':
saveto = os.path.join(args.outputdir, conf_base+'_corner.pdf')
Corner = mcmc_plots.CornerPlot(post, chains, saveplot=saveto)
Corner.plot()
if ptype == 'trend':
nwalkers = status.getint('mcmc', 'nwalkers')
nensembles = status.getint('mcmc', 'nensembles')
saveto = os.path.join(args.outputdir, conf_base+'_trends.pdf')
Trend = mcmc_plots.TrendPlot(post, chains, nwalkers, nensembles, saveto)
Trend.plot()
if ptype == 'derived':
assert status.has_section('derive'), \
"Must run `radvel derive` before plotting derived parameters"
P, _ = radvel.utils.initialize_posterior(config_file)
chains = pd.read_csv(status.get('derive', 'chainfile'))
saveto = os.path.join(
args.outputdir, conf_base+'_corner_derived_pars.pdf'
)
Derived = mcmc_plots.DerivedPlot(chains, P, saveplot=saveto)
Derived.plot()
savestate = {'{}_plot'.format(ptype): os.path.relpath(saveto)}
save_status(statfile, 'plot', savestate)