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Fix a bug of plotter which contains inf #165

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merged 7 commits into from
May 27, 2024
Merged

Fix a bug of plotter which contains inf #165

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463b38a
filter out inf
zihaoxu98 May 27, 2024
c0fa7e2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 27, 2024
61e2f6d
nan filter
zihaoxu98 May 27, 2024
b88cf2d
fix comment
zihaoxu98 May 27, 2024
5e17a50
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 27, 2024
957c81d
change to isfinite
zihaoxu98 May 27, 2024
0ead13a
fix a bug
zihaoxu98 May 27, 2024
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19 changes: 16 additions & 3 deletions appletree/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,23 @@ def __init__(self, backend_file_name, discard=0, thin=1):
backend = emcee.backends.HDFBackend(self.backend_file_name, read_only=True)

self.chain = backend.get_chain(discard=discard, thin=thin)
self.flat_chain = backend.get_chain(discard=discard, thin=thin, flat=True)
self.posterior = backend.get_log_prob(discard=discard, thin=thin)
self.flat_posterior = backend.get_log_prob(discard=discard, thin=thin, flat=True)
self.prior = backend.get_blobs(discard=discard, thin=thin)
# We drop iterations with inf and nan posterior
mask = ~np.isinf(self.posterior) & ~np.isnan(self.posterior)
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https://numpy.org/doc/stable/reference/generated/numpy.isfinite.html

mask = np.all(mask, axis=1)
self.chain = self.chain[mask]
self.posterior = self.posterior[mask]
self.prior = self.prior[mask]

self.flat_chain = backend.get_chain(discard=discard, thin=thin, flat=True)
self.flat_posterior = backend.get_log_prob(discard=discard, thin=thin, flat=True)
self.flat_prior = backend.get_blobs(discard=discard, thin=thin, flat=True)
# We drop samples with inf and nan posterior
mask = ~np.isinf(self.flat_posterior) & ~np.isnan(self.flat_posterior)
self.flat_chain = self.flat_chain[mask]
self.flat_posterior = self.flat_posterior[mask]
self.flat_prior = self.flat_prior[mask]

with h5py.File(self.backend_file_name, "r") as f:
self.param_names = f["mcmc"].attrs["parameter_fit"]
Expand Down Expand Up @@ -199,7 +211,8 @@ def plot_corner(self, fig=None):
if fig is None:
fig = plt.figure(figsize=(2 * (self.n_param + 2), 2 * (self.n_param + 2)))
samples = np.concatenate(
(self.flat_chain, self.flat_posterior[:, None], self.flat_prior[:, None]), axis=1
(self.flat_chain, self.flat_posterior[:, None], self.flat_prior[:, None]),
axis=1,
)
labels = np.concatenate((self.param_names, ["log posterior", "log prior"]))

Expand Down
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