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Bugfix to plot_posterior when plotting extracted posterior files #5188

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Bugfix to plot_posterior when plotting extracted posterior files #5188

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0b3d49d
read in all params instead of variable params when using wildcard; do…
acorreia61201 Sep 19, 2025
91964cf
add functionality to arg parser to avoid unspecified likelihood stats
acorreia61201 Oct 1, 2025
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13 changes: 9 additions & 4 deletions bin/inference/pycbc_inference_plot_posterior
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ from pycbc.results.scatter_histograms import create_multidim_plot
use('agg')

# add options to command line
parser = io.ResultsArgumentParser()
parser = io.ResultsArgumentParser(defaultparams='samples')
pycbc.add_common_pycbc_options(parser)
# program-specific
parser.add_argument("--output-file", type=str, required=True,
Expand All @@ -60,13 +60,18 @@ parser.add_argument("--prior-nsamples", type=int, default=10000,
help="The number of samples to use for plotting the "
"prior. Default is 10000.")
parser.add_argument("--colors-multi-run", nargs="+", type=str,
help="For multiple runs, provide colours to be used for successively. Default setting is to use the successive colours specified in matplotlib color cycle.")
help="For multiple runs, provide colours to be used for "
"successively. Default setting is to use the "
"successive colours specified in matplotlib color "
"cycle.")
parser.add_argument("--fill-hist", action="store_true", default=False,
help="Fill the 1D marginalized histograms")
parser.add_argument("--hist-color",
help="Provide color for histogram outline. Default is black")
help="Provide color for histogram outline. Default is "
"black")
parser.add_argument("--hist-fill-color", default='gray',
help="Provide the fill_color for filled histograms. Default is gray")
help="Provide the fill_color for filled histograms. "
"Default is gray")
# add options for what plots to create
option_utils.add_plot_posterior_option_group(parser)
# scatter configuration
Expand Down
18 changes: 13 additions & 5 deletions pycbc/inference/io/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -446,11 +446,13 @@ class ResultsArgumentParser(argparse.ArgumentParser):
to not be included. May also specify sampler-specific arguments. Note
that ``input-file``, ``file-help``, and ``parameters`` are always
added.
defaultparams : {'variable_params', 'all'}, optional
defaultparams : {'variable_params', 'samples', 'all'}, optional
If no ``--parameters`` provided, which collection of parameters to
load. If 'all' will load all parameters in the file's
``samples_group``. If 'variable_params' or None (the default) will load
the variable parameters.
load. If 'samples' will load all parameters in the file's
``samples_group``, excluding likelihood stats (i.e. loglikelihood,
logwt). If 'all' will load all parameters in the file's
``samples_group`` including likelihood stats. If 'variable_params' or
None (the default) will load the variable parameters.
autoparamlabels : bool, optional
Passed to ``add_results_option_group``; see that function for details.
\**kwargs :
Expand All @@ -462,11 +464,15 @@ def __init__(self, skip_args=None, defaultparams=None,
# add attribute to communicate to arguments what to do when there is
# no input files
self.no_input_file_err = False
self.skip_params = []
if skip_args is None:
skip_args = []
self.skip_args = skip_args
if defaultparams is None:
defaultparams = 'variable_params'
if defaultparams == 'samples':
defaultparams = 'all'
self.skip_params = ['loglikelihood', 'logwt']
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@aleynaakyuz aleynaakyuz Oct 1, 2025

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You’re only skipping two parameters here, but there are other ones that could also be plotted. I plotted result_extracted.hdf here and the result looks like this

self.defaultparams = defaultparams
# add the results option grup
self.add_results_option_group(autoparamlabels=autoparamlabels)
Expand Down Expand Up @@ -510,6 +516,7 @@ def parse_known_args(self, args=None, namespace=None):
if opts.parameters is None or opts.parameters == ['*']:
parameters = get_common_parameters(opts.input_file,
collection=self.defaultparams)
parameters = [i for i in parameters if i not in self.skip_params]
# now call parse parameters action to re-populate the namespace
self.actions['parameters'](self, opts, parameters)
# check if we're being greedy or not
Expand All @@ -526,7 +533,8 @@ def parse_known_args(self, args=None, namespace=None):
add_params = set(all_params) - set(used_params)
# repopulate the name space with the additional parameters
if add_params:
opts.parameters += list(add_params)
add_params = [i for i in add_params if i not in self.skip_params]
opts.parameters += add_params
# update the labels
opts.parameters_labels.update({p: p for p in add_params})
# parse the sampler-specific options and check for any unknowns
Expand Down
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