Merge branch 'fix_dynesty_state_plotting' into 'master'

Fix dynesty state plotting

See merge request !468

CHANGELOG.md

@@ -11,6 +11,8 @@ This breaks backward compatibility.
 The options to `boundary` are `{'periodic', 'reflective', None}`.
 Periodic boundaries are supported as before.
 Reflective boundaries are supported in `dynesty` and `cpnest`.  
+- Added state plotting for dynesty. Use `check_point_plot=True` in the `run_sampler` 
+function to create trace plots during the dynesty checkpoints
 
 ### Removed
 -

bilby/core/sampler/dynesty.py

@@ -5,6 +5,7 @@ import sys
 import pickle
 import signal
 
+import matplotlib.pyplot as plt
 import numpy as np
 from pandas import DataFrame
 
@@ -89,7 +90,7 @@ class Dynesty(NestedSampler):
 
     def __init__(self, likelihood, priors, outdir='outdir', label='label',
                  use_ratio=False, plot=False, skip_import_verification=False,
-                 check_point=True, check_point_plot=False, n_check_point=None,
+                 check_point=True, check_point_plot=True, n_check_point=None,
                  check_point_delta_t=600, resume=True, **kwargs):
         NestedSampler.__init__(self, likelihood=likelihood, priors=priors,
                                outdir=outdir, label=label, use_ratio=use_ratio,
@@ -397,11 +398,20 @@ class Dynesty(NestedSampler):
 
         if plot and self.check_point_plot:
             import dynesty.plotting as dyplot
-            labels = self.search_parameter_keys
-            fn = "{}/{}_checkpoint_trace.png".format(self.outdir, self.label)
-            fig = dyplot.traceplot(self.sampler.results, labels=labels)[0]
-            fig.tight_layout()
-            fig.savefig(fn)
+            labels = [label.replace('_', ' ') for label in self.search_parameter_keys]
+            filename = "{}/{}_checkpoint_trace.png".format(self.outdir, self.label)
+            try:
+                truths = None
+                if self.injection_parameters is not None:
+                    truths = [self.injection_parameters[key] for key in self.search_parameter_keys]
+                fig = dyplot.traceplot(self.sampler.results, labels=labels,
+                                       truths=truths)[0]
+                fig.tight_layout()
+                fig.savefig(filename)
+                plt.close('all')
+            except (RuntimeError, np.linalg.linalg.LinAlgError) as e:
+                logger.warning(e)
+                logger.warning('Failed to create dynesty state plot at checkpoint')
 
     def generate_trace_plots(self, dynesty_results):
         check_directory_exists_and_if_not_mkdir(self.outdir)