From 9c15e3e99867f0e00a91090977fa13d82136df68 Mon Sep 17 00:00:00 2001
From: Gregory Ashton <gregory.ashton@ligo.org>
Date: Wed, 21 Aug 2019 13:47:01 +1000
Subject: [PATCH] Resolve !398 ensures the emcee chains are down selcted
correctly
---
bilby/core/sampler/emcee.py | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index 38878c387..a03dda0b0 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -354,23 +354,23 @@ class Emcee(MCMCSampler):
self.checkpoint()
self.result.sampler_output = np.nan
- blobs_flat = np.array(self.sampler.blobs).reshape((-1, 2))
- log_likelihoods, log_priors = blobs_flat.T
- chain = self.sampler.chain.reshape((-1, self.ndim))
- log_ls = log_likelihoods
- log_ps = log_priors
- self.calculate_autocorrelation(chain)
+
+ self.calculate_autocorrelation(
+ self.sampler.chain.reshape((-1, self.ndim)))
self.print_nburn_logging_info()
self.calc_likelihood_count()
self.result.nburn = self.nburn
- n_samples = self.nwalkers * self.nburn
if self.result.nburn > self.nsteps:
raise SamplerError(
"The run has finished, but the chain is not burned in: "
"`nburn < nsteps`. Try increasing the number of steps.")
- self.result.samples = chain[n_samples:, :]
- self.result.log_likelihood_evaluations = log_ls[n_samples:]
- self.result.log_prior_evaluations = log_ps[n_samples:]
+ self.result.samples = self.sampler.chain[:, self.nburn:, :].reshape(
+ (-1, self.ndim))
+ blobs = np.array(self.sampler.blobs)
+ blobs_trimmed = blobs[self.nburn:, :, :].reshape((-1, 2))
+ log_likelihoods, log_priors = blobs_trimmed.T
+ self.result.log_likelihood_evaluations = log_likelihoods
+ self.result.log_prior_evaluations = log_priors
self.result.walkers = self.sampler.chain
self.result.log_evidence = np.nan
self.result.log_evidence_err = np.nan
--
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