diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1d81bd9ff3d763ed7bafd3cfeccca09b0bebb953..169ab1ac37537eb82430a965d5b658cb33442a5f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ Changes currently on master, but not under a tag.
### Changes
- Make BBH/BNS parameter conversion more logical
- Source frame masses/spins included in posterior
+- Make filling in posterior with fixed parameters work
## [0.3] 2018-01-02
diff --git a/bilby/core/result.py b/bilby/core/result.py
index 7f8d7550610e4774d1983c6af923f6720184c975..ad78abe7d6a852ada6e1df78b2e753ad7305438d 100644
--- a/bilby/core/result.py
+++ b/bilby/core/result.py
@@ -196,6 +196,12 @@ class Result(dict):
if dictionary.get('priors', False):
dictionary['priors'] = {key: str(self.priors[key]) for key in self.priors}
+ # Convert callable kwargs to strings to avoid pickling issues
+ if hasattr(self, 'kwargs'):
+ for key in self.kwargs:
+ if hasattr(self.kwargs[key], '__call__'):
+ self.kwargs[key] = str(self.kwargs[key])
+
try:
deepdish.io.save(file_name, dictionary)
except Exception as e:
@@ -544,12 +550,14 @@ class Result(dict):
if hasattr(self, 'posterior') is False:
data_frame = pd.DataFrame(
self.samples, columns=self.search_parameter_keys)
- data_frame['log_likelihood'] = getattr(
- self, 'log_likelihood_evaluations', np.nan)
for key in priors:
- if getattr(priors[key], 'is_fixed', False):
+ if isinstance(priors[key], DeltaFunction):
data_frame[key] = priors[key].peak
- # We save the samples in the posterior and remove the array of samples
+ elif isinstance(priors[key], float):
+ data_frame[key] = priors[key]
+ data_frame['log_likelihood'] = getattr(
+ self, 'log_likelihood_evaluations', np.nan)
+ # remove the array of samples
del self.samples
else:
data_frame = self.posterior
diff --git a/bilby/core/sampler/base_sampler.py b/bilby/core/sampler/base_sampler.py
index b0d996f3f490fc38406fdd5a84f217cda4bf9abe..fdbc5a32553d2fc3c211a82df07066456dcf384b 100644
--- a/bilby/core/sampler/base_sampler.py
+++ b/bilby/core/sampler/base_sampler.py
@@ -399,6 +399,40 @@ class Sampler(object):
class NestedSampler(Sampler):
npoints_equiv_kwargs = ['nlive', 'nlives', 'n_live_points', 'npoints', 'npoint', 'Nlive']
+ def reorder_loglikelihoods(self, unsorted_loglikelihoods, unsorted_samples,
+ sorted_samples):
+ """ Reorders the stored log-likelihood after they have been reweighted
+
+ This creates a sorting index by matching the reweights `result.samples`
+ against the raw samples, then uses this index to sort the
+ loglikelihoods
+
+ Parameters
+ ----------
+ sorted_samples, unsorted_samples: array
+ Sorted and unsorted values of the samples. These should be of the same
+ shape and contain the same sample values, but in different orders
+ unsorted_loglikelihoods: array
+ The loglikelihoods corresponding to the unsorted_samples
+
+ Returns
+ -------
+ sorted_loglikelihoods: array
+ The loglikelihoods reordered to match that of the sorted_samples
+
+
+ """
+
+ idxs = []
+ for ii in range(len(unsorted_loglikelihoods)):
+ idx = np.where(np.all(sorted_samples[ii] == unsorted_samples, axis=1))
+ if len(idx) > 1:
+ raise ValueError(
+ "Multiple matches found between sorted and unsorted samples")
+ else:
+ idxs.append(idx[0])
+ return unsorted_loglikelihoods[idxs]
+
class MCMCSampler(Sampler):
nwalkers_equiv_kwargs = ['nwalker', 'nwalkers', 'draws']
diff --git a/bilby/core/sampler/dynesty.py b/bilby/core/sampler/dynesty.py
index 62f2171234df56af13660b8caa602b5d6813c525..1f5129992c8527715974ffb2a29938fbd6788e14 100644
--- a/bilby/core/sampler/dynesty.py
+++ b/bilby/core/sampler/dynesty.py
@@ -5,7 +5,7 @@ import sys
import numpy as np
from pandas import DataFrame
from deepdish.io import load, save
-from ..utils import logger
+from ..utils import logger, check_directory_exists_and_if_not_mkdir
from .base_sampler import Sampler, NestedSampler
@@ -164,9 +164,9 @@ class Dynesty(NestedSampler):
out.samples, columns=self.search_parameter_keys)
self.result.nested_samples['weights'] = weights
self.result.nested_samples['log_likelihood'] = out.logl
- idxs = [np.unique(np.where(self.result.samples[ii] == out.samples)[0])
- for ii in range(len(out.logl))]
- self.result.log_likelihood_evaluations = out.logl[idxs]
+ self.result.log_likelihood_evaluations = self.reorder_loglikelihoods(
+ unsorted_loglikelihoods=out.logl, unsorted_samples=out.samples,
+ sorted_samples=self.result.samples)
self.result.log_evidence = out.logz[-1]
self.result.log_evidence_err = out.logzerr[-1]
@@ -282,6 +282,7 @@ class Dynesty(NestedSampler):
sampler: `dynesty.NestedSampler`
NestedSampler to write to disk.
"""
+ check_directory_exists_and_if_not_mkdir(self.outdir)
resume_file = '{}/{}_resume.h5'.format(self.outdir, self.label)
if os.path.isfile(resume_file):
diff --git a/bilby/core/sampler/nestle.py b/bilby/core/sampler/nestle.py
index aa2364462b6120b1bff91089c1f297f7b1c0b6b6..8bcfca7d480192b99e9091babd0c7bf83f2097d9 100644
--- a/bilby/core/sampler/nestle.py
+++ b/bilby/core/sampler/nestle.py
@@ -64,9 +64,9 @@ class Nestle(NestedSampler):
out.samples, columns=self.search_parameter_keys)
self.result.nested_samples['weights'] = out.weights
self.result.nested_samples['log_likelihood'] = out.logl
- idxs = [np.unique(np.where(self.result.samples[ii] == out.samples)[0])
- for ii in range(len(out.logl))]
- self.result.log_likelihood_evaluations = out.logl[idxs]
+ self.result.log_likelihood_evaluations = self.reorder_loglikelihoods(
+ unsorted_loglikelihoods=out.logl, unsorted_samples=out.samples,
+ sorted_samples=self.result.samples)
self.result.log_evidence = out.logz
self.result.log_evidence_err = out.logzerr
return self.result
diff --git a/examples/injection_examples/basic_tutorial.py b/examples/injection_examples/basic_tutorial.py
index f4b5011a53bfa5d7035d1e5816dcd81a1b08fd95..2f3766f8adfd656b63e22b706fe80b5fc54d3bf9 100644
--- a/examples/injection_examples/basic_tutorial.py
+++ b/examples/injection_examples/basic_tutorial.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate running parameter estimation on a reduced parameter
space for an injected signal.
diff --git a/examples/injection_examples/binary_neutron_star_example.py b/examples/injection_examples/binary_neutron_star_example.py
index 4026c966667cc72c09397a33eb221db9e75bfe26..76cf0c1ec9d27f79099f2798df6847a963070ee1 100644
--- a/examples/injection_examples/binary_neutron_star_example.py
+++ b/examples/injection_examples/binary_neutron_star_example.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate running parameter estimation on a binary neutron star
system taking into account tidal deformabilities.
diff --git a/examples/injection_examples/calibration_example.py b/examples/injection_examples/calibration_example.py
index d111d3896bbdc4d2839e79b84c759a9f003254c8..9f2052ffb55d019aa1509ae251aa6f57d4bc9c14 100644
--- a/examples/injection_examples/calibration_example.py
+++ b/examples/injection_examples/calibration_example.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate running parameter estimation with calibration
uncertainties included.
diff --git a/examples/injection_examples/create_your_own_source_model.py b/examples/injection_examples/create_your_own_source_model.py
index f304b97abb0d3e418d8b93ff3a41b4d56e32f3a5..254fdfc52f4dd76aed5df74fbb9b31c79b134787 100644
--- a/examples/injection_examples/create_your_own_source_model.py
+++ b/examples/injection_examples/create_your_own_source_model.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
A script to demonstrate how to use your own source model
"""
diff --git a/examples/injection_examples/create_your_own_time_domain_source_model.py b/examples/injection_examples/create_your_own_time_domain_source_model.py
index ac45e1ef987ec27868d643ce590b74debd481c53..5ea57fb58897f5e0cace5f9a9ad22c40c0ba3afb 100644
--- a/examples/injection_examples/create_your_own_time_domain_source_model.py
+++ b/examples/injection_examples/create_your_own_time_domain_source_model.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
"""
A script to show how to create your own time domain source model.
A simple damped Gaussian signal is defined in the time domain, injected into noise in
diff --git a/examples/injection_examples/eccentric_inspiral.py b/examples/injection_examples/eccentric_inspiral.py
index 235536ca48482e4bf39d6e58f7533f9822f22239..75ff93b572e85f9e2abfae62b341057d9c51b2f3 100644
--- a/examples/injection_examples/eccentric_inspiral.py
+++ b/examples/injection_examples/eccentric_inspiral.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate running parameter estimation on a reduced parameter space
for an injected eccentric binary black hole signal with masses & distnace similar
diff --git a/examples/injection_examples/how_to_specify_the_prior.py b/examples/injection_examples/how_to_specify_the_prior.py
index 706bdaedc1da97fde24db50b10ded0a56ec0c086..b92288d90237f57fceb84b48704ed296e67bf9bf 100644
--- a/examples/injection_examples/how_to_specify_the_prior.py
+++ b/examples/injection_examples/how_to_specify_the_prior.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate how to specify the prior distributions used for parameter estimation.
"""
diff --git a/examples/injection_examples/marginalized_likelihood.py b/examples/injection_examples/marginalized_likelihood.py
index 300649719a3519999ed78eab6256a18f5c98367f..83259d627e80909796d646be386ced0fbd2e2e99 100644
--- a/examples/injection_examples/marginalized_likelihood.py
+++ b/examples/injection_examples/marginalized_likelihood.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate how to improve the speed and efficiency of parameter estimation on an injected signal using
phase and distance marginalisation.
diff --git a/examples/injection_examples/plot_time_domain_data.py b/examples/injection_examples/plot_time_domain_data.py
index d03c3200a4f5303c3ecad0f045701dd0e1521efd..f3d056b7a9a594a328a200c84ac334ec50775093 100644
--- a/examples/injection_examples/plot_time_domain_data.py
+++ b/examples/injection_examples/plot_time_domain_data.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
"""
from __future__ import division, print_function
diff --git a/examples/injection_examples/sine_gaussian_example.py b/examples/injection_examples/sine_gaussian_example.py
index c63691af107ab8b9ac680fe034da0f30b4f5f581..4bbf7c6b0181c28212c26731acbff17539c29f28 100644
--- a/examples/injection_examples/sine_gaussian_example.py
+++ b/examples/injection_examples/sine_gaussian_example.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate running parameter estimation on a sine gaussian injected signal.
diff --git a/examples/injection_examples/using_gwin.py b/examples/injection_examples/using_gwin.py
index f6f0e28d640c45a9fbbc7fe9c47286e9568df0da..a213c490c6a30bd51dda582baa1675b6c300f3c3 100644
--- a/examples/injection_examples/using_gwin.py
+++ b/examples/injection_examples/using_gwin.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
An example of how to use bilby with `gwin` (https://github.com/gwastro/gwin) to
perform CBC parameter estimation.
diff --git a/examples/open_data_examples/GW150914.py b/examples/open_data_examples/GW150914.py
index b0876d243a6634ff76368a72bdcf6cdcf465a625..aa5ca44af19f6575feb8ed7e8b4e373b001bec0a 100644
--- a/examples/open_data_examples/GW150914.py
+++ b/examples/open_data_examples/GW150914.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate running parameter estimation on GW150914 using open
data.
diff --git a/examples/open_data_examples/GW150914_minimal.py b/examples/open_data_examples/GW150914_minimal.py
index 339eb3b13558c9b5f05e31916e150c6db6da3b30..520fe6ae9aa3c7428207e6880660fc62dbc9f827 100644
--- a/examples/open_data_examples/GW150914_minimal.py
+++ b/examples/open_data_examples/GW150914_minimal.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
Tutorial to demonstrate the minimum number of steps required to run parameter
stimation on GW150914 using open data.
diff --git a/examples/other_examples/add_multiple_results.py b/examples/other_examples/add_multiple_results.py
index b4f99ba9669ae95ab7adb3372b007f41fd840086..f4c565555ad6250390622cd71fd1f433a7599c64 100644
--- a/examples/other_examples/add_multiple_results.py
+++ b/examples/other_examples/add_multiple_results.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
An example of running two sets of posterior sample estimations and adding them
"""
diff --git a/examples/other_examples/gaussian_example.py b/examples/other_examples/gaussian_example.py
index 318222e2d1fe62b003bc543ceb5c8c1aedc95d9d..bf7730286f12ddc70ac9bfe647e6e637fd4004ac 100644
--- a/examples/other_examples/gaussian_example.py
+++ b/examples/other_examples/gaussian_example.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
An example of how to use bilby to perform paramater estimation for
non-gravitational wave data consisting of a Gaussian with a mean and variance
diff --git a/examples/other_examples/get_LOSC_event_data.py b/examples/other_examples/get_LOSC_event_data.py
index 7a8836ba110f881e687860a718b0c4092c734a35..6197426eb6e02869fb73e18b349d8dde92ca1fc5 100644
--- a/examples/other_examples/get_LOSC_event_data.py
+++ b/examples/other_examples/get_LOSC_event_data.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
""" Helper script to faciliate downloading data from LOSC
Usage: To download the GW150914 data from https://losc.ligo.org/events/
diff --git a/examples/other_examples/linear_regression_pymc3.py b/examples/other_examples/linear_regression_pymc3.py
index 3328d8cf5722fcb5f3db5047f6d423ff645285f7..c10d5d3c93480254bc6ca2fa4d05ea128f0e2718 100644
--- a/examples/other_examples/linear_regression_pymc3.py
+++ b/examples/other_examples/linear_regression_pymc3.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
An example of how to use bilby to perform paramater estimation for
non-gravitational wave data. In this case, fitting a linear function to
diff --git a/examples/other_examples/linear_regression_pymc3_custom_likelihood.py b/examples/other_examples/linear_regression_pymc3_custom_likelihood.py
index 2f36967947d1ff0d4087758bb3070b8aa37569f9..9321ea4c82621250201b3af8b97484845cd2e9a7 100644
--- a/examples/other_examples/linear_regression_pymc3_custom_likelihood.py
+++ b/examples/other_examples/linear_regression_pymc3_custom_likelihood.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
An example of how to use bilby to perform paramater estimation for
non-gravitational wave data. In this case, fitting a linear function to
diff --git a/examples/other_examples/occam_factor_example.py b/examples/other_examples/occam_factor_example.py
index b164a3298b55fc54ff6225a19136480c63521b73..b977eaeadf53086326ca4047a8a9aa64bb607b0c 100644
--- a/examples/other_examples/occam_factor_example.py
+++ b/examples/other_examples/occam_factor_example.py
@@ -1,4 +1,4 @@
-#!/bin/python
+#!/usr/bin/env python
"""
As part of the :code:`bilby.result.Result` object, we provide a method to