Fix bug in nsamples estimate

bilby/core/sampler/ptemcee.py

@@ -667,6 +667,9 @@ def check_iteration(
     """
 
     ci = convergence_inputs
+    # Note: nsteps is the number of steps in the samples while iterations is
+    # the current iteration number. So iteration > nsteps by the number of
+    # od discards
     nwalkers, nsteps, ndim = samples.shape
 
     tau_array = calculate_tau_array(samples, search_parameter_keys, ci)
@@ -699,14 +702,15 @@ def check_iteration(
     nburn = int(ci.burn_in_nact * tau_int)
     thin = int(np.max([1, ci.thin_by_nact * tau_int]))
     samples_per_check = nwalkers / thin
-    nsamples_effective = int(nwalkers * (iteration - nburn) / thin)
+    nsamples_effective = int(nwalkers * (nsteps - nburn) / thin)
+    print(nwalkers, iteration, nsteps, nburn, thin, nsamples_effective)
 
     # Calculate convergence boolean
     converged = Q < ci.Q_tol and ci.nsamples < nsamples_effective
     logger.debug("Convergence: Q<Q_tol={}, nsamples<nsamples_effective={}"
                  .format(Q < ci.Q_tol, ci.nsamples < nsamples_effective))
 
-    GRAD_WINDOW_LENGTH = 11
+    GRAD_WINDOW_LENGTH = nwalkers + 1
     nsteps_to_check = ci.autocorr_tau * np.max([2 * GRAD_WINDOW_LENGTH, tau_int])
     lower_tau_index = np.max([0, len(tau_list) - nsteps_to_check])
     check_taus = np.array(tau_list[lower_tau_index :])
@@ -990,11 +994,15 @@ def plot_tau(
 def plot_mean_log_likelihood(mean_log_likelihood, outdir, label):
 
     ntemps, nsteps = mean_log_likelihood.shape
+    max_logl = np.max(mean_log_likelihood)
+    ymax = max_logl + 0.01 * np.abs(max_logl)
+    ymin = max_logl - 0.1 * np.abs(max_logl)
 
     fig, ax = plt.subplots()
     idxs = np.arange(nsteps)
     ax.plot(idxs, mean_log_likelihood.T)
-    ax.set(xlabel="Iteration", ylabel=r"$\langle\log\mathcal{L}\rangle$")
+    ax.set(xlabel="Iteration", ylabel=r"$\langle\log\mathcal{L}\rangle$",
+           ylim=(ymin, ymax))
     fig.tight_layout()
     fig.savefig("{}/{}_checkpoint_meanloglike.png".format(outdir, label))
     plt.close(fig)