8. HD 283572 Corner Plot

8.1. Notebook setup

import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import emcee
import corner
import warnings
warnings.filterwarnings('ignore')

8.2. Download data

Unzip the contents into a folder named data in the same level as the notebooks folder. The directory structure should end up looking like the following:

thermal-gs
├── data
│   ├── HD283572_chain.h5
│   ├── HD283572_lmfit_params.txt
│   ├── thermal-gs.mplstyle
│   ├── ...
├── figures
│   ├── HD283572_corner.pdf
│   ├── HD283572_corner.png
│   ├── ...
├── notebooks
│   ├── HD283572_corner-plot.ipynb
│   ├── ...
.
.
.

8.3. Load

sampler = emcee.backends.HDFBackend('../data/HD283572_chain.h5')
samples = sampler.get_chain(flat=True)
samples /= np.array([1, 1, 1, 1, np.pi/180, 1, 1, 1, 1, np.pi/180])
lmfit_params = np.loadtxt('../data/HD283572_lmfit_params.txt')
lmfit_params /= np.array([1, 1, 1, 1, np.pi/180, 1, 1, 1, 1, np.pi/180])

plt.style.use('../data/thermal-gs.mplstyle')

8.4. Plot

thin = 10000
plt_labels = [r'$L_{\rm pwr}$', '$\delta$', r'$n_{e,{\rm pwr}}$', r'$B_{\rm pwr}$', r'$\phi_{\rm pwr}$', r'$L_{\rm th}$', '$T_e$', r'$n_{e,{\rm th}}$', r'$B_{\rm th}$', r'$\phi_{\rm th}$']
median_values = np.median(samples[::thin, :], axis=0)
cmap = mpl.cm.get_cmap('Reds')
cmap.set_under(color='w')

cornerFig = corner.corner(samples[::thin, :],color='black',top_ticks=True,quiet=True, show_titles=True,use_math_text=True,
labels=plt_labels,plot_datapoints=False, title_quantiles=[0.16, 0.5, 0.84], label_kwargs={"fontsize":24}, 
title_kwargs={"fontsize":16}, max_n_ticks=4, bins=25, title_fmt='3.3g', plot_density=False, fill_contours=True,
levels=(0.393, 0.865, 0.989), hist_kwargs={'linewidth':0.75, 'color':cmap(0.75)},
contour_kwargs={'linewidths':0.5, 'colors':'black'}, 
contourf_kwargs={'colors':(cmap(-1), cmap(0.25), cmap(0.75), cmap(0.999)), 'alpha':0.75})

for axis in cornerFig.axes:
    axis.tick_params(axis='both', which='major', labelsize=16)

corner.overplot_lines(cornerFig, lmfit_params, color='C0', label='Least squares')
corner.overplot_points(cornerFig, np.array([lmfit_params]), color='C0', marker='s', ms=5)
corner.overplot_lines(cornerFig, median_values, color='black', label='Median')
corner.overplot_points(cornerFig, np.array([median_values]), color='black', marker='s', ms=5)

handles,labels = cornerFig.gca().get_legend_handles_labels()
by_label = dict(zip(labels, handles))
cornerFig.legend(by_label.values(), by_label.keys(), fontsize=24)
cornerFig.set_facecolor('white')
plt.savefig('../figures/HD283572_corner.png', bbox_inches='tight')
plt.savefig('../figures/HD283572_corner.pdf', bbox_inches='tight')
cornerFig.show()