def plot_dist_corner_getdist(samples,
labels=None,
names=None,
filled=True,
sample_labels=None):
if isinstance(samples, (list, tuple)):
if sample_labels is None:
sample_labels = [
'samples {0:d}'.format(i) for i in range(len(samples))
]
samps = [
MCSamples(samples=samples0,
names=names,
labels=labels,
label=str(slabels0))
for samples0, slabels0 in zip(samples, sample_labels)
]
g = plots.get_subplot_plotter()
g.triangle_plot(samps, filled=filled)
else:
samps = MCSamples(samples=samples, names=names, labels=labels)
g = plots.get_subplot_plotter()
g.triangle_plot(samps, filled=filled)
plt.show()
return None
def testMixtures(self):
from getdist.gaussian_mixtures import Mixture2D, GaussianND
cov1 = [[0.001 ** 2, 0.0006 * 0.05], [0.0006 * 0.05, 0.05 ** 2]]
cov2 = [[0.01 ** 2, -0.005 * 0.03], [-0.005 * 0.03, 0.03 ** 2]]
mean1 = [0.02, 0.2]
mean2 = [0.023, 0.09]
mixture = Mixture2D([mean1, mean2], [cov1, cov2], names=['zobs', 't'], labels=[r'z_{\rm obs}', 't'],
label='Model')
tester = 0.03
cond = mixture.conditionalMixture(['zobs'], [tester])
marge = mixture.marginalizedMixture(['zobs'])
# test P(x,y) = P(y)P(x|y)
self.assertAlmostEqual(mixture.pdf([tester, 0.15]), marge.pdf([tester]) * cond.pdf([0.15]))
samples = mixture.MCSamples(3000, label='Samples', random_state=10)
g = plots.get_subplot_plotter()
g.triangle_plot([samples, mixture], filled=False)
g.new_plot()
g.plot_1d(cond, 't')
s1 = 0.0003
covariance = [[s1 ** 2, 0.6 * s1 * 0.05, 0], [0.6 * s1 * 0.05, 0.05 ** 2, 0.2 ** 2], [0, 0.2 ** 2, 2 ** 2]]
mean = [0.017, 1, -2]
gauss = GaussianND(mean, covariance)
g = plots.get_subplot_plotter()
g.triangle_plot(gauss, filled=True)
def test_specifics(self):
testdists = Test2DDistributions()
samples = testdists.bimodal[0].MCSamples(1000, logLikes=True, random_state=10)
g = plots.get_subplot_plotter(auto_close=True)
g.settings.prob_label = r'$P$'
g.settings.prob_y_ticks = True
g.plot_1d(samples, 'x', _no_finish=True)
ax = g.get_axes()
self.assertTrue(np.allclose(ax.get_yticks(), [0, 0.5, 1]), "Wrong probability ticks")
def check_ticks(bounds, expected):
ax.set_xlim(bounds)
ticks = ax.get_xticks()
if len(ticks) != len(expected) or not np.allclose(ticks, expected):
raise self.failureException("Wrong ticks %s for bounds %s" % (ticks, bounds))
check_ticks([-5.2, 5.2], [-4, -2, 0, 2, 4])
check_ticks([0, 8.2], [0, 2, 4, 6, 8])
check_ticks([0.0219, 0.02232], [0.022, 0.0222])
check_ticks([-0.009, 0.009], [-0.008, 0., 0.008])
g.make_figure(nx=2, ny=1, sharey=True)
ax = g.get_axes()
g._set_main_axis_properties(ax.xaxis, True)
ax.set_yticks([])
check_ticks([-0.009, 0.009], [-0.006, 0., 0.006])
check_ticks([1, 1.0004], [1.0001, 1.0003])
def newGraph_Confidence(result):
H_0 = [ii[0] for ii in result]
omega_m0 = [ii[1] for ii in result]
omega_q0 = [ii[2] for ii in result]
alpha = [ii[3] for ii in result]
alpha_x = [ii[4] for ii in result]
m = [ii[5] for ii in result]
names = [
"H_0", "\Omega_{m_0}", "\Omega_{Q_0}", r"\tilde{\alpha}",
r"\tilde{\alpha}_x", "m"
]
#names = ["H_0"]
labels = names
newShape = [H_0, omega_m0, omega_q0, alpha, alpha_x, m]
#newShape = [H_0]
values = np.array(newShape).T
#print(values.shape)
s1 = MCSamples(samples=values, names=names, labels=labels)
g = plots.get_subplot_plotter()
s1.updateSettings({'contours': [0.68, 0.95, 0.99]})
g.settings.colormap = "binary"
g.settings.num_plot_contours = 3
g.triangle_plot([s1], shaded=True, title_limit=1)
plt.savefig("result.pdf")
def Eval(model, q_x_z, training_dataset, results_dir):
approximate_posterior = training_dataset.copy(label=r"$q_x(x)$")
approximate_posterior.samples = q_x_z.sample(training_dataset.samples.shape[0]).numpy()
g = plots.get_subplot_plotter(width_inch=6.5)
g.triangle_plot([training_dataset, approximate_posterior], ['omegabh2', 'omegach2', 'theta', 'tau', 'omegak', 'logA', 'ns'], filled=True)
g.export(str(results_dir / "densities" / "corner.pdf"))
return
def plot3D(self, pp, colorn=None, contour_num=2, **kwargs):
if colorn:
colorss = colors[colorn - 1:colorn - 1 + self._n]
else:
colorss = None
if pp == 0:
t_name = self.param_names
else:
t_name = []
for i in pp:
t_name.append(self.param_names[i - 1])
g = plots.get_subplot_plotter(width_inch=9)
g.settings.num_plot_contours = contour_num
g.settings.legend_fontsize = 20
g.settings.axes_fontsize = 14
g.settings.lab_fontsize = 18
g.settings.figure_legend_frame = False
g.settings.alpha_filled_add = 0.8
if all(self.lengend):
print(t_name)
g.triangle_plot(self.Samp,
t_name,
filled_compare=True,
legend_labels=self.lengend,
contour_colors=colorss,
legend_loc='upper right',
**kwargs)
else:
g.triangle_plot(self.Samp,
t_name,
filled_compare=True,
contour_colors=colorss,
**kwargs)
if 'tline' in kwargs:
for ax in g.subplots[:, 0]:
ax.axvline(kwargs['tline'], color='k', ls='--', alpha=0.5)
# plt.tight_layout()
if 'ax_range' in kwargs:
for axi in kwargs['ax_range']:
g.subplots[-1, axi[0] - 1].xaxis.set_major_locator(
plt.MultipleLocator(axi[1]))
if axi[0] - 1 > 0:
g.subplots[axi[0] - 1, 0].yaxis.set_major_locator(
plt.MultipleLocator(axi[1]))
if 'xlim' in kwargs:
for xi in kwargs['xlim']:
for ax in g.subplots[:, xi[0] - 1]:
if ax is not None:
ax.set_xlim(xi[1][0], xi[1][1])
if 'name' in kwargs:
g.export(os.path.join(outdir, '%s.pdf' % kwargs['name']))
else:
g.export(os.path.join(outdir, ''.join(self.root) + '_tri.pdf'))
return g
def cornerplot(sampledf, weights=None, labels=None, markers=None, ranges=None):
names = sampledf.columns
samples = MCSamples(samples=sampledf.to_numpy(),
names=names,
weights=weights,
labels=labels,
ranges=ranges)
#samples.updateSettings({'contours': [0.68, 0.95, 0.99]})
g = plots.get_subplot_plotter()
return g.triangle_plot(samples, filled=True, markers=markers)
def Plot1D_Omegak_H0_Omegam(results_dir):
labels = [
"base_omegak_plikHM_TTTEEE_lowl_lowE",
"base_omegak_plikHM_TTTEEE_lowl_lowE_BAO"
]
datasets = [LoadDataset(label) for label in labels]
g = plots.get_subplot_plotter(width_inch=5)
g.settings.figure_legend_frame = False
g.plots_1d(datasets, ['omegak', 'H0', 'omegam'], nx=3, legend_labels=["PlikHM TTTEEE+lowl+lowE", "+BAO"], legend_ncol=2)
g.export(str(results_dir / "1D_omegak_H0_omegam.pdf"))
return
def plot_corner(results, outprefix=None, **kwargs):
"""
Store a simple corner plot in outprefix_corner.pdf, based on samples
extracted from fit.
Additional kwargs are passed to MCSamples.
"""
la = get_flat_posterior(results)
samples = []
paramnames = []
badlist = ['lp__']
badlist += [
k for k in la.keys()
if 'log' in k and k.replace('log', '') in la.keys()
]
for k in sorted(la.keys()):
print('%20s: %.4f +- %.4f' % (k, la[k].mean(), la[k].std()))
if k not in badlist and la[k].ndim == 2:
samples.append(la[k])
paramnames.append(k)
if len(samples) == 0:
arrays = [
k for k in la.keys()
if la[k].ndim == 3 and la[k].shape[2] <= 20 and k not in badlist
]
if len(arrays) != 1:
warnings.warn("no scalar variables found")
return
k = arrays[0]
# flatten across chains and column for each variable
samples = la[k]
paramnames = ['%s[%d]' % (k, i + 1) for i in range(la[k].shape[1])]
samples = numpy.transpose(samples)
import matplotlib.pyplot as plt
from getdist import MCSamples, plots
settings = kwargs.pop('settings', dict(smooth_scale_2D=3.0))
samples_g = MCSamples(samples=samples,
names=paramnames,
settings=settings,
**kwargs)
g = plots.get_subplot_plotter()
g.settings.num_plot_contours = 3
g.triangle_plot([samples_g],
filled=False,
contour_colors=plt.cm.Set1.colors)
if outprefix is not None:
plt.savefig(outprefix + '_corner.pdf', bbox_inches='tight')
plt.close()
def plot_multicomp_velo_2corr(store,
group_name,
outname='velo_2corr',
truths=None):
group = store.hdf[group_name]
ncomp = group.attrs['ncomp']
assert ncomp == 2
n_params = store.hdf.attrs['n_params']
post = group['posteriors'][...][:, :-2] # param values
par_names = store.model.get_par_names(ncomp)
ix_v = store.model.IX_VCEN
ix_s = store.model.IX_SIGM
par_labels = [''] * n_params * ncomp
par_labels[ncomp *
ix_v] = r'$v_\mathrm{lsr}\, (1) \ [\mathrm{km\,s^{-1}}]$'
par_labels[ncomp * ix_v +
1] = r'$v_\mathrm{lsr}\, (2) \ [\mathrm{km\,s^{-1}}]$'
par_labels[ncomp *
ix_s] = r'$\sigma_\mathrm{v}\, (1) \ [\mathrm{km\,s^{-1}}]$'
par_labels[ncomp * ix_s +
1] = r'$\sigma_\mathrm{v}\, (2) \ [\mathrm{km\,s^{-1}}]$'
samples = getdist.MCSamples(samples=post,
names=par_names,
labels=par_labels,
sampler='nested')
samples.updateSettings({'contours': [0.68, 0.90]})
fig = gd_plt.get_subplot_plotter()
x_names = ['v1', 's1']
y_names = ['v2', 's2']
if truths is not None:
xmarkers = {k: truths[k] for k in x_names}
ymarkers = {k: truths[k] for k in y_names}
else:
xmarkers, ymarkers = None, None
fig.rectangle_plot(x_names,
y_names,
roots=samples,
filled=True,
line_args={
'lw': 2,
'color': 'peru'
},
xmarkers=xmarkers,
ymarkers=ymarkers)
fig.export(f'{outname}.pdf')
plt.close('all')
def triangulo(datos, labels = []):
'''
DESCRIPTION: Esta funcion realiza una grafica triangular para visualizar los resultados
IN: datos = lista con puntos de datos (cada uno es una lista con valores para cada parametro)
labels = nombre de los parametros (default p_i)
OUT: Grafica triangular con histogramas 1d y 2d de todas la combinaciones
'''
g = plots.get_subplot_plotter(subplot_size=2)
#Checamos si se asignó nombre a los parametros
if labels!=[]:
samples = MCSamples(samples=np.array(datos), labels = labels, names = labels)
else:
samples = MCSamples(samples=np.array(datos))
#graficamos
g.triangle_plot(samples, filled=True, title_limit=1)
def plot_corner(group, outname='corner', truths=None):
ncomp = group.attrs['ncomp']
par_labels = ammonia.TEX_LABELS.copy()
par_labels[3] = r'$\log(N) \ [\log(\mathrm{cm^{-2}})]$'
n_params = group.attrs['n_params'] // ncomp
names = ammonia.get_par_names()
post = group['posteriors'][...][:, :-2] # posterior param values
if truths is not None:
markers = {
p: truths[i * ncomp:(i + 1) * ncomp]
for i, p in zip(range(n_params), ammonia.get_par_names())
}
else:
markers = None
# Give each model component parameter set its own sampler object so that
# each can be over-plotted in its own color.
samples = [
getdist.MCSamples(samples=post[:, ii::ncomp],
names=names,
labels=par_labels,
label=f'Component {ii+1}',
name_tag=f'{ii}',
sampler='nested') for ii in range(ncomp)
]
[s.updateSettings({'contours': [0.68, 0.90]}) for s in samples]
fig = gd_plt.get_subplot_plotter()
fig.triangle_plot(
samples,
filled=True,
line_args=[{
'lw': 2,
'color': 'tab:orange'
}, {
'lw': 2,
'color': 'tab:blue'
}, {
'lw': 2,
'color': 'tab:green'
}],
markers=markers,
)
fig.export(f'{outname}.pdf')
plt.close('all')
def plot_corner(store, group_name, outname='corner', truths=None):
n_params = store.hdf.attrs['n_params']
par_names = store.model.get_par_names()
par_labels = store.hdf.attrs['tex_labels_with_units']
group = store.hdf[group_name]
ncomp = group.attrs['ncomp']
post = group['posteriors'][...][:, :-2] # posterior param values
if truths is not None:
markers = {
p: truths[i * ncomp:(i + 1) * ncomp]
for i, p in zip(range(n_params), par_names)
}
else:
markers = None
# Give each model component parameter set its own sampler object so that
# each can be over-plotted in its own color.
samples = [
getdist.MCSamples(samples=post[:, ii::ncomp],
names=par_names,
labels=par_labels,
label=f'Component {ii+1}',
name_tag=f'{ii}',
sampler='nested') for ii in range(ncomp)
]
[s.updateSettings({'contours': [0.68, 0.90]}) for s in samples]
fig = gd_plt.get_subplot_plotter()
fig.triangle_plot(
samples,
filled=True,
line_args=[{
'lw': 2,
'color': 'tab:orange'
}, {
'lw': 2,
'color': 'tab:blue'
}, {
'lw': 2,
'color': 'tab:green'
}],
markers=markers,
)
fig.export(f'{outname}.pdf')
plt.close('all')
def triangle_plot(list_of_obj, **kwargs):
# if isinstance(list_of_obj, list):
# for obj in list_of_obj:
# print(obj.sampler)
# exit()
plotter = plots.get_subplot_plotter(width_inch=12, )
# NOTE:
plotter.settings.num_plot_contours = 2
plotter.triangle_plot(list_of_obj,
legend_labels=kwargs["legend_labels"],
line_args=kwargs["line_args"],
contour_args=kwargs["contour_args"],
markers=kwargs["markers"],
legend_loc='upper right',
legend_kwargs={"fontsize": 20})
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
from getdist import plots
mpl.use("Agg")
freq = [90, 150, 220]
spec_in_freq = {}
spec_in_freq[90] = ["dr6_pa5_f090", "dr6_pa6_f090"]
spec_in_freq[150] = ["dr6_pa4_f150", "dr6_pa5_f150", "dr6_pa6_f150"]
spec_in_freq[220] = ["dr6_pa4_f220"]
for f in freq:
roots = []
for spec in spec_in_freq[f]:
roots += ["mcmc_%s" % spec]
params = ["eps_min", "lmax", "beta"]
g = plots.get_subplot_plotter(
chain_dir=os.path.join(os.getcwd(), "chains"),
analysis_settings={"ignore_rows": 0.3},
)
kwargs = dict(colors=["k"], lws=[1])
g.triangle_plot(roots, params, **kwargs, diag1d_kwargs=kwargs)
g.subplots[0, 0].plot([], [], color="k", label="PSpipe")
g.subplots[0, 0].legend(loc="upper left", bbox_to_anchor=(1, 1))
plt.savefig("chain_results_%s.png" % f)
'm1': [mod1low, mod1up],
'm2': [mod2low, mod2up]
}) #,weights=1/10**first)#,loglikes=like)
else:
samples = MCSamples(samples=samps,
names=names,
labels=labels,
ranges={'m1': [mod1low, mod1up]})
elif (np.any(il == 5)):
ai, = np.where(il == 5)
names[ai] = 'm2'
samples = MCSamples(samples=samps,
names=names,
labels=labels,
ranges={'m2': [mod2low, mod2up]}) #,loglikes=like)
g = plots.get_subplot_plotter(width_inch=7.5)
g.settings.axes_fontsize = 20
g.settings.axes_labelsize = 20
g.triangle_plot([samples], filled=True, color='red')
mpl.show()
print(r"Confidence interval at 2$\sigma$")
print(samples.getTable().tableTex())
elif total == 3:
first = data[:, il[0]]
second = data[:, il[1]]
third = data[:, il[2]]
samps = np.column_stack((first, second, third))
ndim = 3
names = np.array(["x%s" % i for i in range(ndim)])
labels = label[il]
#%%
%matplotlib qt5
ndim = 4
names = ['M_{abs}','\Omega_{m}','b','H_{0}']
labels=names
samples1 = MCSamples(samples=samples_1,names = names, labels = labels,ranges={'b':[0, None]})
samples1 = samples1.copy(label=r'Lowest-order with $0.3\sigma$ smoothing',
settings={'mult_bias_correction_order':0,'smooth_scale_2D':0.3, 'smooth_scale_1D':0.3})
samples2 = MCSamples(samples=samples_2,names = names, labels = labels,ranges={'b':[0, None]})
samples2 = samples2.copy(label=r'Lowest-order with $0.3\sigma$ smoothing',
settings={'mult_bias_correction_order':0,'smooth_scale_2D':0.3, 'smooth_scale_1D':0.3})
samples3 = MCSamples(samples=samples_3,names = names, labels = labels,ranges={'b':[0, None]})
samples3 = samples3.copy(label=r'Lowest-order with $0.3\sigma$ smoothing',
settings={'mult_bias_correction_order':0,'smooth_scale_2D':0.3, 'smooth_scale_1D':0.3})
samples0 = MCSamples(samples=samples_0,names = names, labels = labels,ranges={'b':[0, None]})
samples0 = samples0.copy(label=r'Lowest-order with $0.3\sigma$ smoothing',
settings={'mult_bias_correction_order':0,'smooth_scale_2D':0.3, 'smooth_scale_1D':0.3})
g = plots.get_subplot_plotter()
g.triangle_plot([samples0, samples1, samples2, samples3],
contour_colors=['grey','g','r','b'],
filled=True, params = names ,
contour_lws=1.5,
# param_limits = dict
legend_labels = ['CC+SN', 'CC+SN+AGN', 'CC+SN+BAO','CC+SN+BAO+AGN'])
plt.savefig('/home/matias/Desktop/contornos_EXP.png')
def plot_contours_dynesty(chaintags,
legend_labels=None,
params_toplot=None,
colors=None,
legend_loc='upper center',
legend_fontsize=20,
vertical_markers=None,
vertical_marker_color='grey'):
bounds = utils.get_emulator_bounds()
sample_arr = []
for i, chaintag in enumerate(chaintags):
chain_fn = f'../chains/chains_{chaintag}.h5'
fw = h5py.File(chain_fn, 'r')
param_names = fw.attrs['param_names']
if vertical_markers is None:
vertical_markers_toplot = fw.attrs['true_values']
else:
vertical_markers_toplot = vertical_markers
fw.close()
pickle_fn = f'{pickle_dir}/results_{chaintag}.pkl'
with open(pickle_fn, 'rb') as pf:
res = pickle.load(pf)
samples = res['samples']
lnweight = np.array(res['logwt'])
lnevidence = np.array(res['logz'])
if params_toplot is not None:
idxs = []
for pm in params_toplot:
idxs.append(np.where(param_names == pm))
idxs = np.array(idxs).flatten()
samples = samples[:, idxs]
# weight and evidence are for all parameters, shape (n_samps,)
# so don't need to slice
param_names = params_toplot
vertical_markers_toplot = vertical_markers_toplot[idxs]
labels = [param_labels[pn] for pn in param_names]
ranges = [bounds[pn] for pn in param_names]
#[-1] bc just care about final evidence value
weights = np.exp(lnweight - lnevidence[-1])
weights = weights.flatten()
samps = MCSamples(names=param_names, labels=labels)
samps.setSamples(samples, weights=weights)
sample_arr.append(samps)
marker_args = {'color': vertical_marker_color}
g = plots.get_subplot_plotter()
g.settings.alpha_filled_add = 0.4
g.settings.figure_legend_frame = False
g.settings.legend_fontsize = legend_fontsize
g.settings.axis_marker_lw = 1.0
g.settings.axis_marker_color = 'dimgrey'
g.triangle_plot(sample_arr,
filled=True,
contour_colors=colors,
names=param_names,
legend_labels=legend_labels,
markers=vertical_markers_toplot,
title_limit=1,
legend_loc=legend_loc,
marker_args=marker_args,
axis_marker_color='red')
return g
def plot_contours(chaintags,
legend_labels=None,
params_toplot=None,
nsteps=None,
colors=None,
legend_loc='upper center',
legend_fontsize=20,
weight_with_dynesty=False):
bounds = utils.get_emulator_bounds()
sample_arr = []
for i, chaintag in enumerate(chaintags):
resample_chains = False
if 'dynesty' in chaintag:
resample_chains = True
assert not (nsteps != None and resample_chains
), "if resampling, shouldn't be selecting nsteps!"
chain_fn = f'../chains/chains_{chaintag}.h5'
fw = h5py.File(chain_fn, 'r')
chain_dset = fw['chain']
chain = np.array(chain_dset)
print(chaintag, ':', chain.shape)
if nsteps:
chain = chain[:, :nsteps, :]
lnprob_dset = fw['lnprob']
param_names = fw.attrs['param_names']
true_values = fw.attrs['true_values']
if params_toplot is not None:
idxs = []
for pm in params_toplot:
idxs.append(np.where(param_names == pm))
idxs = np.array(idxs).flatten()
chain = chain[:, :, idxs]
param_names = params_toplot
true_values = true_values[idxs]
nwalkers, nchain, ndim = chain.shape
samples = chain.reshape(-1, chain.shape[-1])
labels = [param_labels[pn] for pn in param_names]
ranges = [bounds[pn] for pn in param_names]
if resample_chains:
lnweight_dset = fw['lnweight']
lnevidence_dset = fw['lnevidence']
#[-1] bc just care about final evidence value
lnweight = np.array(lnweight_dset)[0] #[0] bc an extra array dim
lnevidence = np.array(lnevidence_dset)[0]
weights = np.exp(lnweight - lnevidence[-1])
weights = weights.flatten()
samples = np.empty((nchain, ndim))
for nd in range(ndim):
cn = chain[:, :, nd].flatten()
if weight_with_dynesty:
samples[:, nd] = dynesty.utils.resample_equal(cn, weights)
else:
samples[:, nd] = cn
else:
weights = None
fw.close()
if weight_with_dynesty:
weights = None
# have not gotten ranges to work
samps = MCSamples(names=param_names, labels=labels, ranges=ranges)
# for some reason get slightly diff answer if don't use setSamples and pass them straight to MCSamples!
samps.setSamples(samples, weights=weights)
sample_arr.append(samps)
g = plots.get_subplot_plotter()
g.settings.alpha_filled_add = 0.4
g.settings.figure_legend_frame = False
g.settings.legend_fontsize = legend_fontsize
g.settings.axis_marker_lw = 1.0
g.settings.axis_marker_color = 'dimgrey'
g.triangle_plot(
sample_arr,
filled=True,
contour_colors=colors,
names=param_names,
legend_labels=legend_labels,
markers=true_values,
title_limit=1,
legend_loc=legend_loc,
#marker_args={'color': 'orange', 'lw':1.5}
)
return g
# Export the results to GetDist
from getdist.mcsamples import MCSamplesFromCobaya
gd_sample = MCSamplesFromCobaya(updated_info, sampler.products()["sample"])
# Analyze and plot
mean = gd_sample.getMeans()[:2]
covmat = gd_sample.getCovMat().matrix[:2, :2]
print("Mean:")
print(mean)
print("Covariance matrix:")
print(covmat)
# %matplotlib inline # uncomment if running from the Jupyter notebook
import getdist.plots as gdplt
gdplot = gdplt.get_subplot_plotter()
gdplot.triangle_plot(gd_sample, ["a", "b"], filled=True)
def run_test_program(plots=('dists_2D', 'dists_1D'),
sims=100,
nsamp=default_nsamp,
mbc=1,
bco=1):
import time
chains.print_load_details = False
plt.rc("ytick", direction="in")
plt.rc("xtick", direction="in")
test1D = Test1DDistributions()
test2D = Test2DDistributions()
test_settings = {
'mult_bias_correction_order': mbc,
'boundary_correction_order': bco,
'smooth_scale_1D': -1,
'smooth_scale_2D': -1
}
g = get_subplot_plotter(subplot_size=2)
colors = ['k', 'C0', 'C1', 'C2', 'C3', 'C4']
if 'ISE_1D' in plots:
compare_method(test1D.distributions(),
nx=3,
test_settings=[
{
'mult_bias_correction_order': 1,
'boundary_correction_order': 1
},
{
'mult_bias_correction_order': 2,
'boundary_correction_order': 1
},
{
'mult_bias_correction_order': 0,
'boundary_correction_order': 0
},
{
'mult_bias_correction_order': 0,
'boundary_correction_order': 1
},
{
'mult_bias_correction_order': 0,
'boundary_correction_order': 2
},
],
colors=colors,
linestyles=['-', '-', ':', '-.', '--'],
fname='compare_method_1d_N%s.pdf' % nsamp,
sims=sims,
nsamp=nsamp)
if 'ISE_2D' in plots:
compare_method(test2D.distributions(),
nx=4,
test_settings=[
{
'mult_bias_correction_order': 1,
'boundary_correction_order': 1
},
{
'mult_bias_correction_order': 2,
'boundary_correction_order': 1
},
{
'mult_bias_correction_order': 0,
'boundary_correction_order': 0
},
{
'mult_bias_correction_order': 0,
'boundary_correction_order': 1
},
],
colors=colors,
linestyles=['-', '-', ':', '-.', '--'],
fname='compare_method_2d_N%s.pdf' % nsamp,
sims=sims,
nsamp=nsamp)
if plots is None or 'dists_1D' in plots:
g.new_plot()
start = time.time()
compare1D(g,
test1D.distributions(),
nsamp=nsamp,
settings=test_settings)
print('1D timing:', time.time() - start)
join_subplots(g.subplots)
plt.savefig('test_dists_1D_mbc%s_bco%s_N%s.pdf' % (mbc, bco, nsamp),
bbox_inches='tight')
if plots is None or 'dists_2D' in plots:
g.new_plot()
start = time.time()
compare2D(g,
test2D.distributions(),
nsamp=nsamp,
settings=test_settings)
print('2D timing:', time.time() - start)
join_subplots(g.subplots)
plt.savefig('test_dists_2D_mbc%s_bco%s_N%s.pdf' % (mbc, bco, nsamp),
bbox_inches='tight')
from getdist import plots
import matplotlib.pyplot as plt
g = plots.get_subplot_plotter(chain_dir=r'/home/app/Git/LCDM-NS/cobaya')
roots = []
roots.append('cobaya without SSIM/run')
roots.append('cobaya with SSIM - CSD3/run')
roots.append('cobaya with iPPR - CSD3/run')
# roots.append('cobaya with SSIM - PC/run')
params = ['logA', 'n_s', 'theta_s_1e2', 'omega_b', 'omega_cdm', 'tau_reio']
g.triangle_plot(roots, params, filled=True, colors=['blue', 'grey', 'red'])
g.export()
plt.savefig('../illustrations/cosmology.pdf')
plt.show()
roots = []
roots.append('cobaya with SSIM - CSD3/run')
# roots.append('cobaya with iPPR - CSD3/run')
# roots.append('cobaya without SSIM/run')
roots.append('cobaya with SSIM - PC/run')
params = ['logA', 'n_s', 'theta_s_1e2', 'omega_b', 'omega_cdm', 'tau_reio']
g.triangle_plot(roots, params, filled=True, colors=['grey', 'orange'])
g.export()
plt.savefig('../illustrations/cosmo-pc.pdf')
plt.show()
ranges={'d':(d_min, d_max), \
'm_1':(m_min_bh, m_max_bh), \
'm_2':(m_min_ns, m_max_ns), \
'm_c':(m_c_min, m_c_max), \
'q_inv':(q_inv_min, q_inv_max)}, \
label='SMF Priors')
bgw_gds = gd.MCSamples(samples=bgw_samples, \
names=['d', 'm_1', 'm_2', 'm_c', 'q_inv'], \
labels=[r'D_L', 'm_1', 'm_2', 'M_c', '1/q'], \
ranges={'d':(d_min, d_max), \
'm_1':(m_min_bh_bgw, m_max_bh_bgw), \
'm_2':(m_min_ns_bgw, m_max_ns_bgw), \
'm_c':(m_c_min, m_c_max), \
'q_inv':(q_inv_min, q_inv_max)}, \
label='Bilby Priors')
g = gdp.get_subplot_plotter()
g.settings.lw_contour = lw
cm = mpcm.get_cmap('plasma')
g.triangle_plot([bgw_gds, smf_gds], filled=True, \
line_args=[{'lw':lw, 'color':'C0'}, \
{'lw':lw, 'color':'C1'}], \
colors=['C0', 'C1'])
n_pars = smf_samples.shape[1]
for i in range(n_pars):
for j in range(0, i + 1):
g.subplots[i, j].grid(False)
plot_file = outdir + '/' + label + '_bilby_prior_comp.pdf'
g.export(plot_file)
exit()
# calculate tidal deformabilities for all NSs
def main(args):
np.random.seed(2)
Ndata = args.ndata
jitter_true = 0.1
phase_true = 2.0
period_true = 180
amplitude_true = args.contrast / Ndata * jitter_true
paramnames = ['amplitude', 'jitter', 'phase', 'period']
ndim = len(paramnames)
x = np.linspace(0, 360, 1000)
y = amplitude_true * sin(x / period_true * 2 * pi + phase_true)
if True:
plt.plot(x, y)
x = np.random.uniform(0, 360, Ndata)
y = np.random.normal(amplitude_true * sin(x / period_true * 2 * pi + phase_true), jitter_true)
plt.errorbar(x, y, yerr=jitter_true, marker='x', ls=' ')
plt.savefig('testsine.pdf', bbox_inches='tight')
plt.close()
def loglike(params):
amplitude, jitter, phase, period = params
predicty = amplitude * sin(x / period * 2 * pi + phase)
logl = (-0.5 * log(2 * pi * jitter**2) - 0.5 * ((predicty - y) / jitter)**2).sum()
return logl
def transform(x):
z = np.empty_like(x)
z[0] = 10**(x[0] * 4 - 2)
z[1] = 10**(x[1] * 1 - 1.5)
z[2] = 2 * pi * x[2]
z[3] = 10**(x[3] * 4 - 1)
#z[:,4] = 2 * pi / x[:,3]
return z
loglike(transform(np.ones(ndim)*0.5))
from snowline import ReactiveImportanceSampler
sampler = ReactiveImportanceSampler(paramnames, loglike, transform=transform)
sampler.run()
sampler.print_results()
from getdist import MCSamples, plots
samples_g = MCSamples(samples=sampler.results['samples'],
names=sampler.results['paramnames'],
label='Gaussian',
settings=dict(smooth_scale_2D=3), sampler='nested')
mcsamples = [samples_g]
g = plots.get_subplot_plotter(width_inch=8)
g.settings.num_plot_contours = 3
g.triangle_plot(mcsamples, filled=False, contour_colors=plt.cm.Set1.colors)
plt.savefig('testsine_posterior.pdf', bbox_inches='tight')
plt.close()
# Just plotting (loading on-the-fly) import getdist.plots as gdplt import os folder, name = os.path.split(os.path.abspath(info["output"])) gdplot = gdplt.get_subplot_plotter(chain_dir=folder) gdplot.triangle_plot(name, ["a", "b"], filled=True)
#samples = loadMCSamples(chainLoadSample, settings={'ignore_rows':0.3})
# It was already burned
samples = loadMCSamples(chainLoadSample)
# C5::
# PDF files of the posteriors:
posteriors = download_dir + posteriors_dir + fileStr + "_histograms.pdf"
# C6::
# PDF files of the confidence regions files:
confidenceL = download_dir + confidenceL_dir + fileStr + "_confidence.pdf"
# C7::
# Multiple 1D subplots
g = plots.get_subplot_plotter(width_inch=10)
# Plot and save to a file:
g.plots_1d(samples, ['p1', 'p2', 'p3', 'p4', 'p5', 'p6'], nx=6)
g.export(posteriors)
# C8::
# Multiple 2D subplots
g = plots.get_subplot_plotter(subplot_size=2.0)
g.settings.scaling = False # prevent scaling down font sizes even though small subplots
# Plot and save to a file:
g.plots_2d(samples,
param_pairs=[['p1', 'p2'], ['p1', 'p3'], ['p1', 'p4'], ['p2', 'p3'],
['p2', 'p4'], ['p3', 'p4']],
nx=6,
plt.subplots_adjust(bottom=0.175, left=0.175, hspace=0, wspace=0)
print('Saving...')
plt.savefig(
'/Users/hattifattener/Documents/y3cosmicshear/plots/1x2pt_external_maglim.pdf'
)
plt.savefig(
'/Users/hattifattener/Documents/y3cosmicshear/plots/1x2pt_external_maglim.png'
)
plt.close()
from getdist import plots, MCSamples
import getdist
import matplotlib.pyplot as plt
g = plots.get_subplot_plotter() #(width_inch=6, ratio=1)
g.settings.legend_fontsize = 18
g.settings.fontsize = 18
g.settings.axes_fontsize = 18
g.settings.axes_labelsize = 22
g.settings.axis_tick_max_labels = 15
g.settings.linewidth = 1.5
g.settings.legend_colored_text = True
g.settings.axis_tick_step_groups = [[2.5, 3, 4, 6, 8], [1, 2, 5, 10]]
samples = MCSamples(samples=samp0.T,
names=['x1', 'x2', 'x3'],
labels=names,
label='DES Y3',
weights=c0.weight,
settings={
def testPlots(self):
self.samples = self.testdists.bimodal[0].MCSamples(12000, logLikes=True, random_state=10)
g = plots.get_single_plotter(auto_close=True)
samples = self.samples
p = samples.getParams()
samples.addDerived(p.x + (5 + p.y) ** 2, name='z')
samples.addDerived(p.x, name='x.yx', label='forPattern')
samples.addDerived(p.y, name='x.2', label='x_2')
samples.updateBaseStatistics()
g.plot_1d(samples, 'x')
g.new_plot()
g.plot_1d(samples, 'y', normalized=True, marker=0.1, marker_color='b')
g.new_plot()
g.plot_2d(samples, 'x', 'y')
g.new_plot()
g.plot_2d(samples, 'x', 'y', filled=True)
g.new_plot()
g.plot_2d(samples, 'x', 'y', shaded=True)
g.new_plot()
g.plot_2d_scatter(samples, 'x', 'y', color='red', colors=['blue'])
g.new_plot()
g.plot_3d(samples, ['x', 'y', 'z'])
g = plots.get_subplot_plotter(width_inch=8.5, auto_close=True)
g.plots_1d(samples, ['x', 'y'], share_y=True)
g.new_plot()
g.triangle_plot(samples, ['x', 'y', 'z'])
self.assertTrue(g.get_axes_for_params('x', 'z') == g.subplots[2, 0])
self.assertTrue(g.get_axes_for_params('z', 'x', ordered=False) == g.subplots[2, 0])
self.assertTrue(g.get_axes_for_params('x') == g.subplots[0, 0])
self.assertTrue(g.get_axes_for_params('x', 'p', 'q') is None)
self.assertTrue(g.get_axes(ax=('x', 'z')) == g.subplots[2, 0])
self.assertTrue(g.get_axes(ax=(2, 0)) == g.subplots[2, 0])
g.new_plot()
g.triangle_plot(samples, ['x', 'y'], plot_3d_with_param='z')
g.new_plot()
g.rectangle_plot(['x', 'y'], ['z'], roots=samples, filled=True)
prob2 = self.testdists.bimodal[1]
samples2 = prob2.MCSamples(12000, random_state=10)
g.new_plot()
g.triangle_plot([samples, samples2], ['x', 'y'])
g.new_plot()
g.plots_2d([samples, samples2], param_pairs=[['x', 'y'], ['x', 'z']])
g.new_plot()
g.plots_2d([samples, samples2], 'x', ['z', 'y'])
g.new_plot()
self.assertEqual([name.name for name in samples.paramNames.parsWithNames('x.*')], ['x.yx', 'x.2'])
g.triangle_plot(samples, 'x.*')
samples.updateSettings({'contours': '0.68 0.95 0.99'})
g.settings.num_plot_contours = 3
g.plot_2d(samples, 'x', 'y', filled=True)
g.add_y_bands(0.2, 1.5)
g.add_x_bands(-0.1, 1.2, color='red')
g.new_plot()
omm = np.arange(0.1, 0.7, 0.01)
g.add_bands(omm, 0.589 * omm ** (-0.25), 0.03 * omm ** (-0.25), nbands=3)
g = plots.get_subplot_plotter()
import copy
for upper in [False, True]:
g.triangle_plot([samples, samples2], ['x', 'y', 'z'], filled=True,
upper_roots=[copy.deepcopy(samples)], upper_kwargs={'contour_colors': ['green']},
legend_labels=['1', '2', '3'], upper_label_right=upper)
for i in range(3):
for j in range(i):
self.assertTrue(g.subplots[i, j].get_xlim() == g.subplots[j, i].get_ylim())
self.assertTrue(g.subplots[i, j].get_ylim() == g.subplots[j, i].get_xlim())
self.assertTrue(g.subplots[i, j].get_xlim() == g.subplots[j, j].get_xlim())
