From 4c6bb18c4db71b736d6741a972222a2061209f2f Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Tue, 20 Apr 2021 11:39:12 +0100
Subject: [PATCH 01/13] improving doc strings and logger messages

---
 pesummary/core/file/formats/bilby.py      |  4 +--
 pesummary/core/file/read.py               | 43 ++++++++++++++---------
 pesummary/gw/file/formats/bilby.py        | 18 +++++++++-
 pesummary/gw/file/formats/default.py      |  3 ++
 pesummary/gw/file/formats/lalinference.py |  3 ++
 pesummary/io/read.py                      | 17 +++++++--
 6 files changed, 67 insertions(+), 21 deletions(-)

diff --git a/pesummary/core/file/formats/bilby.py b/pesummary/core/file/formats/bilby.py
index 6ec2fec7..1d3658fe 100644
--- a/pesummary/core/file/formats/bilby.py
+++ b/pesummary/core/file/formats/bilby.py
@@ -356,10 +356,10 @@ class Bilby(SingleAnalysisRead):
         return kwargs
 
     @staticmethod
-    def _grab_data_from_bilby_file(path, **kwargs):
+    def _grab_data_from_bilby_file(path, function=read_bilby, **kwargs):
         """Load the results file using the `bilby` library
         """
-        return read_bilby(path, **kwargs)
+        return function(path, **kwargs)
 
     def add_marginalized_parameters_from_config_file(self, config_file):
         """Search the configuration file and add the marginalized parameters
diff --git a/pesummary/core/file/read.py b/pesummary/core/file/read.py
index 26573e2b..bc3b5402 100644
--- a/pesummary/core/file/read.py
+++ b/pesummary/core/file/read.py
@@ -10,26 +10,45 @@ import os
 __author__ = ["Charlie Hoy <charlie.hoy@ligo.org>"]
 
 
-def is_bilby_hdf5_file(path):
-    """Determine if the results file is a bilby hdf5 results file
+def _check_bilby_file(f):
+    """Determine if the results file is a bilby results file
 
     Parameters
     ----------
-    path: str
-        path to the results file
+    f: dict-like
+        loaded result file
     """
-    import h5py
     try:
-        f = h5py.File(path, "r")
         if "bilby" in f["version"]:
             return True
         elif "bilby" in str(f["version"][0]):
             return True
         else:
+            standard_keys = [
+                "fixed_parameter_keys", "label", "posterior", "meta_data",
+                "outdir", "parameter_labels"
+            ]
+            if all(key in f.keys() for key in standard_keys):
+                logger.info(
+                    "This file looks like a bilby result file but unable "
+                    "to find the string 'bilby' in the version information."
+                )
             return False
     except Exception:
         return False
-    return False
+
+
+def is_bilby_hdf5_file(path):
+    """Determine if the results file is a bilby hdf5 results file
+
+    Parameters
+    ----------
+    path: str
+        path to the results file
+    """
+    import h5py
+    f = h5py.File(path, "r")
+    return _check_bilby_file(f)
 
 
 def is_bilby_json_file(path):
@@ -43,15 +62,7 @@ def is_bilby_json_file(path):
     import json
     with open(path, "r") as f:
         data = json.load(f)
-    try:
-        if "bilby" in data["version"]:
-            return True
-        elif "bilby" in data["version"][0]:
-            return True
-        else:
-            return False
-    except Exception:
-        return False
+    return _check_bilby_file(data)
 
 
 def _is_pesummary_hdf5_file(path, check_function):
diff --git a/pesummary/gw/file/formats/bilby.py b/pesummary/gw/file/formats/bilby.py
index 99c5ea12..03835807 100644
--- a/pesummary/gw/file/formats/bilby.py
+++ b/pesummary/gw/file/formats/bilby.py
@@ -80,6 +80,12 @@ class Bilby(GWSingleAnalysisRead):
         distributions. Default False
     pe_algorithm: str
         name of the algorithm used to generate the posterior samples
+    disable_injection_conversion: Bool, optional
+        if True, disable the conversion module from deriving alternative
+        injection parameters
+    add_zero_likelihood: Bool, optional
+        if True assign 'log_likelihood=0' to every sample if no 'log_likelihood'
+        samples can be found. Default True
 
     Attributes
     ----------
@@ -265,7 +271,17 @@ class Bilby(GWSingleAnalysisRead):
         Complex matched filter SNRs are stored in the result file.
         The amplitude and angle are extracted here.
         """
-        return read_bilby(path, disable_prior=disable_prior, **kwargs)
+        try:
+            return CoreBilby._grab_data_from_bilby_file(
+                path, function=read_bilby, disable_prior=disable_prior,
+                **kwargs
+            )
+        except Exception as e:
+            logger.warn(
+                "Although the file '{}' passed the bilby file check, we "
+                "were unable to load the file because {}.".format(path, e)
+            )
+            raise
 
     def add_marginalized_parameters_from_config_file(self, config_file):
         """Search the configuration file and add the marginalized parameters
diff --git a/pesummary/gw/file/formats/default.py b/pesummary/gw/file/formats/default.py
index 6726c6db..841b5654 100644
--- a/pesummary/gw/file/formats/default.py
+++ b/pesummary/gw/file/formats/default.py
@@ -17,6 +17,9 @@ class SingleAnalysisDefault(GWSingleAnalysisRead):
     ----------
     path_to_results_file: str
         path to the results file you wish to load
+    add_zero_likelihood: Bool, optional
+        if True assign 'log_likelihood=0' to every sample if no 'log_likelihood'
+        samples can be found. Default True
 
     Attributes
     ----------
diff --git a/pesummary/gw/file/formats/lalinference.py b/pesummary/gw/file/formats/lalinference.py
index a9773438..65df1a00 100644
--- a/pesummary/gw/file/formats/lalinference.py
+++ b/pesummary/gw/file/formats/lalinference.py
@@ -90,6 +90,9 @@ class LALInference(GWSingleAnalysisRead):
     ----------
     path_to_results_file: str
         path to the results file you wish to load in with `LALInference`
+    add_zero_likelihood: Bool, optional
+        if True assign 'log_likelihood=0' to every sample if no 'log_likelihood'
+        samples can be found. Default True
 
     Attributes
     ----------
diff --git a/pesummary/io/read.py b/pesummary/io/read.py
index 977939a2..fc8995ca 100644
--- a/pesummary/io/read.py
+++ b/pesummary/io/read.py
@@ -3,6 +3,7 @@
 import os
 import importlib
 from pathlib import Path
+from pesummary.utils.decorators import docstring_subfunction
 from pesummary.core.file.formats.ini import read_ini
 from pesummary.core.file.formats.pickle import read_pickle
 from pesummary.gw.file.formats.lcf import read_lcf
@@ -33,6 +34,18 @@ def _fetch_from_remote_server(ff):
     return path
 
 
+@docstring_subfunction(
+    [
+        "pesummary.core.file.formats.bilby.Bilby",
+        "pesummary.core.file.formats.default.Default",
+        "pesummary.core.file.formats.pesummary.PESummary",
+        "pesummary.gw.file.formats.bilby.Bilby",
+        "pesummary.gw.file.formats.GWTC1.GWTC1",
+        "pesummary.gw.file.formats.lalinference.LALInference",
+        "pesummary.gw.file.formats.pesummary.PESummary",
+        "pesummary.gw.file.formats.pesummary.TGRPESummary"
+    ]
+)
 def read(
     path, package="gw", file_format=None, skymap=False, cls=None,
     checkpoint=False, **kwargs
@@ -56,8 +69,8 @@ def read(
     checkpoint: Bool, optional
         if True, treat path as the path to a checkpoint file
     **kwargs: dict, optional
-        all additional kwargs are passed to the `pesummary.{}.file.read.read`
-        function
+        all additional kwargs are passed to the
+        `pesummary.{}.file.formats.{}.{}` class. See below for details
     """
     if not os.path.isfile(path) and "@" in path:
         path = _fetch_from_remote_server(path)
-- 
GitLab


From 96be73725b8e9e278f382a0fbef00220455a3255 Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Tue, 20 Apr 2021 11:50:47 +0100
Subject: [PATCH 02/13] typo

---
 pesummary/core/file/formats/bilby.py |  9 ++++++++-
 pesummary/gw/file/formats/bilby.py   | 15 ++++-----------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/pesummary/core/file/formats/bilby.py b/pesummary/core/file/formats/bilby.py
index 1d3658fe..a398548a 100644
--- a/pesummary/core/file/formats/bilby.py
+++ b/pesummary/core/file/formats/bilby.py
@@ -359,7 +359,14 @@ class Bilby(SingleAnalysisRead):
     def _grab_data_from_bilby_file(path, function=read_bilby, **kwargs):
         """Load the results file using the `bilby` library
         """
-        return function(path, **kwargs)
+        try:
+            return function(path, **kwargs)
+        except Exception as e:
+            raise Exception(
+                "Although the file passed the bilby file check, we were "
+                "unable to load the file because {}. This could be because "
+                "of a bilby version incompatability".format(e)
+            )
 
     def add_marginalized_parameters_from_config_file(self, config_file):
         """Search the configuration file and add the marginalized parameters
diff --git a/pesummary/gw/file/formats/bilby.py b/pesummary/gw/file/formats/bilby.py
index 03835807..6355f559 100644
--- a/pesummary/gw/file/formats/bilby.py
+++ b/pesummary/gw/file/formats/bilby.py
@@ -271,17 +271,10 @@ class Bilby(GWSingleAnalysisRead):
         Complex matched filter SNRs are stored in the result file.
         The amplitude and angle are extracted here.
         """
-        try:
-            return CoreBilby._grab_data_from_bilby_file(
-                path, function=read_bilby, disable_prior=disable_prior,
-                **kwargs
-            )
-        except Exception as e:
-            logger.warn(
-                "Although the file '{}' passed the bilby file check, we "
-                "were unable to load the file because {}.".format(path, e)
-            )
-            raise
+        return CoreBilby._grab_data_from_bilby_file(
+            path, function=read_bilby, disable_prior=disable_prior,
+            **kwargs
+        )
 
     def add_marginalized_parameters_from_config_file(self, config_file):
         """Search the configuration file and add the marginalized parameters
-- 
GitLab


From 03b802d98e529d1ddd0d75deb05aa8f60eca5b2e Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Tue, 20 Apr 2021 11:56:34 +0100
Subject: [PATCH 03/13] typo

---
 pesummary/core/file/formats/bilby.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/pesummary/core/file/formats/bilby.py b/pesummary/core/file/formats/bilby.py
index a398548a..51c9299a 100644
--- a/pesummary/core/file/formats/bilby.py
+++ b/pesummary/core/file/formats/bilby.py
@@ -363,9 +363,12 @@ class Bilby(SingleAnalysisRead):
             return function(path, **kwargs)
         except Exception as e:
             raise Exception(
-                "Although the file passed the bilby file check, we were "
-                "unable to load the file because {}. This could be because "
-                "of a bilby version incompatability".format(e)
+                "Although the file looks like it was produced with bilby, we "
+                "were unable to load the file with the "
+                "'bilby.core.result.read_in_result' function because {}. This "
+                "is likely a result of a bilby version incompatability".format(
+                    e
+                )
             )
 
     def add_marginalized_parameters_from_config_file(self, config_file):
-- 
GitLab


From 9bb8f3e0f733d39dc6d15c2041a62f72afdde63a Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Tue, 20 Apr 2021 14:22:20 +0100
Subject: [PATCH 04/13] change kwarg to match command line argument

---
 pesummary/cli/summarycombine_posteriors.py |  2 +-
 pesummary/cli/summaryextract.py            |  3 +-
 pesummary/cli/summaryjscompare.py          |  2 +-
 pesummary/core/file/formats/bilby.py       | 12 ++++---
 pesummary/core/inputs.py                   |  3 +-
 pesummary/gw/file/formats/bilby.py         | 15 ++++----
 pesummary/gw/inputs.py                     |  5 +--
 pesummary/tests/read_test.py               |  4 +--
 pesummary/utils/decorators.py              | 40 ++++++++++++++++++++++
 9 files changed, 66 insertions(+), 20 deletions(-)

diff --git a/pesummary/cli/summarycombine_posteriors.py b/pesummary/cli/summarycombine_posteriors.py
index c8cdb937..399d3eeb 100644
--- a/pesummary/cli/summarycombine_posteriors.py
+++ b/pesummary/cli/summarycombine_posteriors.py
@@ -76,7 +76,7 @@ def main(args=None):
         label: samples for label, samples in zip(opts.labels, opts.samples)
     }
     mydict = MultiAnalysisSamplesDict.from_files(
-        samples, disable_prior=True, disable_injection_conversion=True
+        samples, disable_prior_sampling=True, disable_injection_conversion=True
     )
     combined = mydict.combine(
         use_all=opts.use_all, weights=opts.weights, labels=opts.labels,
diff --git a/pesummary/cli/summaryextract.py b/pesummary/cli/summaryextract.py
index 4d7ec9bd..75ff182c 100644
--- a/pesummary/cli/summaryextract.py
+++ b/pesummary/cli/summaryextract.py
@@ -51,7 +51,8 @@ def main(args=None):
     opts, unknown = _parser.parse_known_args(args=args)
     logger.info("Loading file: '{}'".format(opts.samples))
     f = read(
-        opts.samples, disable_prior=True, disable_injection_conversion=True
+        opts.samples, disable_prior_sampling=True,
+        disable_injection_conversion=True
     )
     posterior_samples = f.samples_dict
     logger.info("Writing analysis: '{}' to file".format(opts.label))
diff --git a/pesummary/cli/summaryjscompare.py b/pesummary/cli/summaryjscompare.py
index fe40ba13..f3348f62 100644
--- a/pesummary/cli/summaryjscompare.py
+++ b/pesummary/cli/summaryjscompare.py
@@ -36,7 +36,7 @@ _check_latex_install()
 
 def load_data(data_file):
     """ Read in a data file and return samples dictionary """
-    f = read(data_file, package="gw", disable_prior=True)
+    f = read(data_file, package="gw", disable_prior_sampling=True)
     return f.samples_dict
 
 
diff --git a/pesummary/core/file/formats/bilby.py b/pesummary/core/file/formats/bilby.py
index 51c9299a..84c12336 100644
--- a/pesummary/core/file/formats/bilby.py
+++ b/pesummary/core/file/formats/bilby.py
@@ -6,13 +6,15 @@ from pesummary.core.file.formats.base_read import SingleAnalysisRead
 from pesummary.core.plots.latex_labels import latex_labels
 from pesummary import conf
 from pesummary.utils.utils import logger
+from pesummary.utils.decorators import deprecated_kwargs
 
 __author__ = ["Charlie Hoy <charlie.hoy@ligo.org>"]
 
 
+@deprecated_kwargs({"disable_prior": "disable_prior_sampling"})
 def read_bilby(
-    path, disable_prior=False, complex_params=[], latex_dict=latex_labels,
-    nsamples_for_prior=None, **kwargs
+    path, disable_prior_sampling=False, complex_params=[],
+    latex_dict=latex_labels, nsamples_for_prior=None, **kwargs
 ):
     """Grab the parameters and samples in a bilby file
 
@@ -20,7 +22,7 @@ def read_bilby(
     ----------
     path: str
         path to the result file you wish to read in
-    disable_prior: Bool, optional
+    disable_prior_sampling: Bool, optional
         if True, do not collect prior samples from the `bilby` result file.
         Default False
     complex_params: list, optional
@@ -95,7 +97,7 @@ def read_bilby(
             data["config"] = {
                 "config": bilby_object.meta_data["command_line_args"]
             }
-    if not disable_prior:
+    if not disable_prior_sampling:
         logger.debug("Drawing prior samples from bilby result file")
         if nsamples_for_prior is None:
             nsamples_for_prior = len(samples)
@@ -293,7 +295,7 @@ class Bilby(SingleAnalysisRead):
     ----------
     path_to_results_file: str
         path to the results file that you wish to read in with `bilby`.
-    disable_prior: Bool, optional
+    disable_prior_sampling: Bool, optional
         if True, do not collect prior samples from the `bilby` result file.
         Default False
 
diff --git a/pesummary/core/inputs.py b/pesummary/core/inputs.py
index 26e9a123..b51c5ced 100644
--- a/pesummary/core/inputs.py
+++ b/pesummary/core/inputs.py
@@ -223,7 +223,8 @@ class _Input(object):
             `generate_all_posterior_samples` method
         """
         f = read_function(
-            file, file_format=file_format, disable_prior=disable_prior_sampling,
+            file, file_format=file_format,
+            disable_prior_sampling=disable_prior_sampling,
             nsamples_for_prior=nsamples_for_prior, path_to_samples=path_to_samples
         )
         if config is not None:
diff --git a/pesummary/gw/file/formats/bilby.py b/pesummary/gw/file/formats/bilby.py
index 6355f559..054c6ed0 100644
--- a/pesummary/gw/file/formats/bilby.py
+++ b/pesummary/gw/file/formats/bilby.py
@@ -11,7 +11,7 @@ __author__ = ["Charlie Hoy <charlie.hoy@ligo.org>"]
 
 
 def read_bilby(
-    path, disable_prior=False, latex_dict=GWlatex_labels,
+    path, disable_prior_sampling=False, latex_dict=GWlatex_labels,
     complex_params=["matched_filter_snr", "optimal_snr"], **kwargs
 ):
     """Grab the parameters and samples in a bilby file
@@ -20,7 +20,7 @@ def read_bilby(
     ----------
     path: str
         path to the result file you wish to read in
-    disable_prior: Bool, optional
+    disable_prior_sampling: Bool, optional
         if True, do not collect prior samples from the `bilby` result file.
         Default False
     complex_params: list, optional
@@ -35,8 +35,8 @@ def read_bilby(
     )
 
     return _read_bilby(
-        path, disable_prior=disable_prior, latex_dict=latex_dict,
-        complex_params=complex_params, **kwargs
+        path, disable_prior_sampling=disable_prior_sampling,
+        latex_dict=latex_dict, complex_params=complex_params, **kwargs
     )
 
 
@@ -72,7 +72,7 @@ class Bilby(GWSingleAnalysisRead):
     ----------
     path_to_results_file: str
         path to the results file that you wish to read in with `bilby`.
-    disable_prior: Bool, optional
+    disable_prior_sampling: Bool, optional
         if True, do not collect prior samples from the `bilby` result file.
         Default False
     disable_prior_conversion: Bool, optional
@@ -264,7 +264,7 @@ class Bilby(GWSingleAnalysisRead):
         return strain_data
 
     @staticmethod
-    def _grab_data_from_bilby_file(path, disable_prior=False, **kwargs):
+    def _grab_data_from_bilby_file(path, disable_prior_sampling=False, **kwargs):
         """
         Load the results file using the `bilby` library
 
@@ -272,7 +272,8 @@ class Bilby(GWSingleAnalysisRead):
         The amplitude and angle are extracted here.
         """
         return CoreBilby._grab_data_from_bilby_file(
-            path, function=read_bilby, disable_prior=disable_prior,
+            path, function=read_bilby,
+            disable_prior_sampling=disable_prior_sampling,
             **kwargs
         )
 
diff --git a/pesummary/gw/inputs.py b/pesummary/gw/inputs.py
index 8ef012f7..4077f5b3 100644
--- a/pesummary/gw/inputs.py
+++ b/pesummary/gw/inputs.py
@@ -370,7 +370,7 @@ class _GWInput(_Input):
                 if i in _opened.keys() and _opened[i] is not None:
                     f = self._open_result_files[i]
                 else:
-                    f = GWRead(i, disable_prior=True)
+                    f = GWRead(i, disable_prior_sampling=True)
                 try:
                     calibration_data = f.calibration_data_in_results_file
                 except Exception:
@@ -1322,7 +1322,8 @@ class IMRCTInput(_Input):
     def samples(self, samples):
         from pesummary.utils.samples_dict import MultiAnalysisSamplesDict
         self._read_samples = {
-            _label: GWRead(_path, disable_prior=True) for _label, _path in zip(
+            _label: GWRead(_path, disable_prior_sampling=True) for
+            _label, _path in zip(
                 self.labels, self.result_files
             )
         }
diff --git a/pesummary/tests/read_test.py b/pesummary/tests/read_test.py
index 1afdc36c..c9329aa5 100644
--- a/pesummary/tests/read_test.py
+++ b/pesummary/tests/read_test.py
@@ -654,7 +654,7 @@ class BilbyFile(BaseRead):
         """
         for param, prior in self.result.priors["samples"].items():
             assert isinstance(prior, np.ndarray)
-        f = read_function(self.path, disable_prior=True)
+        f = read_function(self.path, disable_prior_sampling=True)
         assert not len(f.priors["samples"])
         f = read_function(self.path, nsamples_for_prior=200)
         params = list(f.priors["samples"].keys())
@@ -1558,7 +1558,7 @@ class TestGWJsonBilbyFile(GWBaseRead):
         assert "final_mass_source_non_evolved" in self.result.priors["samples"].keys()
         f = read_function(self.path, disable_prior_conversion=True)
         assert "final_mass_source_non_evolved" not in f.priors["samples"].keys()
-        f = read_function(self.path, disable_prior=True)
+        f = read_function(self.path, disable_prior_sampling=True)
         assert not len(f.priors["samples"])
         f = read_function(self.path, nsamples_for_prior=200)
         params = list(f.priors["samples"].keys())
diff --git a/pesummary/utils/decorators.py b/pesummary/utils/decorators.py
index 7813e057..ac30c657 100644
--- a/pesummary/utils/decorators.py
+++ b/pesummary/utils/decorators.py
@@ -269,3 +269,43 @@ def deprecation(warning):
             return func(*args, **kwargs)
         return wrapper_function
     return decorator
+
+
+def deprecated_kwargs(deprecated):
+    """Print a warning indicating that a kwarg may be deprecated in future
+    releases
+
+    Parameters
+    ----------
+    deprecated: dict
+        dictionary of kwargs to be deprecated. The key should be the deprecated
+        kwarg and the value should be the new kwarg
+
+    Examples
+    --------
+    >>> @deprecated_kwargs({"n_samples": "nsamples"})
+    ... def uniform_samples(nsamples=1000):
+    ...     return np.random.uniform(size=nsamples)
+    ...
+    >>> np.random.seed(123456789)
+    >>> samples = uniform_samples(n_samples=2000)
+    pesummary/utils/decorators.py:302: UserWarning: n_samples will be deprecated
+    in future releases. Please use nsamples
+      "{}".format(_deprecated_kwarg, _new_kwarg)
+    >>> samples = uniform_samples(nsamples=2000)
+    """
+    def decorator(func):
+        @functools.wraps(func)
+        def wrapper_function(*args, **kwargs):
+            import warnings
+            for _deprecated_kwarg, _new_kwarg in deprecated.items():
+                if _deprecated_kwarg in kwargs.keys():
+                    warnings.warn(
+                        "{} will be deprecated in future releases. Please use "
+                        "{}".format(_deprecated_kwarg, _new_kwarg)
+                    )
+                    val = kwargs.pop(_deprecated_kwarg)
+                    kwargs[_new_kwarg] = val
+            return func(*args, **kwargs)
+        return wrapper_function
+    return decorator
-- 
GitLab


From 6116d1c3a06100efac549ccb8bc455f4933cddaf Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Tue, 20 Apr 2021 17:01:45 +0100
Subject: [PATCH 05/13] add extra kwargs to control the conversion kwargs

---
 pesummary/gw/file/formats/base_read.py | 27 ++++++++++++++++++--------
 pesummary/gw/file/formats/bilby.py     |  6 ++++++
 2 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/pesummary/gw/file/formats/base_read.py b/pesummary/gw/file/formats/base_read.py
index ab3c2e85..18e067ae 100644
--- a/pesummary/gw/file/formats/base_read.py
+++ b/pesummary/gw/file/formats/base_read.py
@@ -78,7 +78,7 @@ def _add_log_likelihood(parameters, samples):
 
 def convert_injection_parameters(
     data, extra_kwargs={"sampler": {}, "meta_data": {}}, disable_convert=False,
-    sampled_parameters=None
+    sampled_parameters=None, **kwargs
 ):
     """Apply the conversion module to the injection data
 
@@ -93,6 +93,8 @@ def convert_injection_parameters(
     sampled_parameters: list, optional
         optional list of sampled parameters. If there is no injection value for
         a given sampled parameter, add a 'nan'
+    **kwargs: dict, optional
+        all kwargs passed to the pesummary.gw.conversions.convert function
     """
     import math
 
@@ -113,7 +115,9 @@ def convert_injection_parameters(
     for i in nan_inds[::-1]:
         parameters.remove(parameters[i])
         samples[0].remove(samples[0][i])
-    inj_samples = convert(parameters, samples, extra_kwargs=extra_kwargs)
+    inj_samples = convert(
+        parameters, samples, extra_kwargs=extra_kwargs, **kwargs
+    )
     if sampled_parameters is not None:
         for i in sampled_parameters:
             if i not in list(inj_samples.keys()):
@@ -198,7 +202,10 @@ class GWRead(Read):
         if self.injection_parameters is not None:
             self.injection_parameters = self.convert_injection_parameters(
                 self.injection_parameters, extra_kwargs=self.extra_kwargs,
-                disable_convert=kwargs.get("disable_injection_conversion", False)
+                disable_convert=kwargs.get("disable_injection_conversion", False),
+                **kwargs.get(
+                    "injection_conversion_kwargs", {}
+                )
             )
         if self.priors is not None and len(self.priors):
             if self.priors["samples"] != {}:
@@ -206,10 +213,12 @@ class GWRead(Read):
                 self.priors["samples"] = self.convert_and_translate_prior_samples(
                     priors, disable_convert=kwargs.get(
                         "disable_prior_conversion", False
-                    )
+                    ), **kwargs.get("prior_conversion_kwargs", {})
                 )
 
-    def convert_and_translate_prior_samples(self, priors, disable_convert=False):
+    def convert_and_translate_prior_samples(
+        self, priors, disable_convert=False, **kwargs
+    ):
         """
         """
         default_parameters = list(priors.keys())
@@ -222,7 +231,7 @@ class GWRead(Read):
         )
         if not disable_convert:
             return convert(
-                parameters, samples, extra_kwargs=self.extra_kwargs
+                parameters, samples, extra_kwargs=self.extra_kwargs, **kwargs
             )
         return SamplesDict(parameters, samples)
 
@@ -586,7 +595,7 @@ class GWSingleAnalysisRead(GWRead, SingleAnalysisRead):
 
     def convert_injection_parameters(
         self, data, extra_kwargs={"sampler": {}, "meta_data": {}},
-        disable_convert=False
+        disable_convert=False, **kwargs
     ):
         """Apply the conversion module to the injection data
 
@@ -598,10 +607,12 @@ class GWSingleAnalysisRead(GWRead, SingleAnalysisRead):
             optional kwargs to pass to the conversion module
         disable_convert: Bool, optional
             if True, do not convert injection parameters
+        **kwargs: dict, optional
+            all kwargs passed to the pesummary.gw.conversions.convert function
         """
         return convert_injection_parameters(
             data, extra_kwargs=extra_kwargs, disable_convert=disable_convert,
-            sampled_parameters=self.parameters
+            sampled_parameters=self.parameters, **kwargs
         )
 
     def to_lalinference(self, **kwargs):
diff --git a/pesummary/gw/file/formats/bilby.py b/pesummary/gw/file/formats/bilby.py
index 054c6ed0..a75dfff2 100644
--- a/pesummary/gw/file/formats/bilby.py
+++ b/pesummary/gw/file/formats/bilby.py
@@ -86,6 +86,12 @@ class Bilby(GWSingleAnalysisRead):
     add_zero_likelihood: Bool, optional
         if True assign 'log_likelihood=0' to every sample if no 'log_likelihood'
         samples can be found. Default True
+    injection_conversion_kwargs: dict, optional
+        optional kwargs to pass to the pesummary.gw.conversions.convert function
+        for the injection parameters
+    prior_conversion_kwargs: dict, optional
+        optional kwargs to pass to the pesummary.gw.conversions.convert function
+        for the prior posteriors
 
     Attributes
     ----------
-- 
GitLab


From 687113cce8254fbbe73d891cf0c0f58a3574dd08 Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Tue, 20 Apr 2021 17:16:28 +0100
Subject: [PATCH 06/13] typo

---
 pesummary/gw/file/formats/bilby.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pesummary/gw/file/formats/bilby.py b/pesummary/gw/file/formats/bilby.py
index a75dfff2..f4fc3105 100644
--- a/pesummary/gw/file/formats/bilby.py
+++ b/pesummary/gw/file/formats/bilby.py
@@ -91,7 +91,7 @@ class Bilby(GWSingleAnalysisRead):
         for the injection parameters
     prior_conversion_kwargs: dict, optional
         optional kwargs to pass to the pesummary.gw.conversions.convert function
-        for the prior posteriors
+        for the prior distributions
 
     Attributes
     ----------
-- 
GitLab


From 8a84b4f3bc238f596a353ba2837ea1b4ff906b44 Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Fri, 30 Apr 2021 00:07:21 +0100
Subject: [PATCH 07/13] adding generate_all_prior_samples,
 generate_all_posterior_samples, generate_all_injection_samples and convert
 methods

---
 pesummary/gw/file/formats/base_read.py    | 309 +++++++++++++++-------
 pesummary/gw/file/formats/bilby.py        |   9 +
 pesummary/gw/file/formats/default.py      |  24 ++
 pesummary/gw/file/formats/lalinference.py |   9 +
 pesummary/gw/file/formats/pesummary.py    |   9 +
 5 files changed, 261 insertions(+), 99 deletions(-)

diff --git a/pesummary/gw/file/formats/base_read.py b/pesummary/gw/file/formats/base_read.py
index b19836ef..239cc303 100644
--- a/pesummary/gw/file/formats/base_read.py
+++ b/pesummary/gw/file/formats/base_read.py
@@ -101,6 +101,10 @@ def convert_injection_parameters(
     if disable_convert:
         return data
     if all(math.isnan(data[i]) for i in data.keys()):
+        if sampled_parameters is not None:
+            for i in sampled_parameters:
+                if i not in list(data.keys()):
+                    data[i] = float("nan")
         return data
     parameters = list(data.keys())
     samples = [[data[i] for i in parameters]]
@@ -163,6 +167,15 @@ class GWRead(Read):
     generate_all_posterior_samples:
         generate all posterior distributions that may be derived from
         sampled distributions
+    generate_all_prior_samples:
+        generate all prior distributions that may be derived from the
+        stored prior distributions
+    generate_all_injection_samples:
+        generate all injection values that may be derived from the stored
+        injection values
+    convert:
+        convert either the posterior distributions, prior distribution and/or
+        the injection samples.
     """
     def __init__(self, path_to_results_file, **kwargs):
         super(GWRead, self).__init__(path_to_results_file, **kwargs)
@@ -199,41 +212,30 @@ class GWRead(Read):
             }
         )
         super(GWRead, self).load(function, _data=data, **kwargs)
-        if self.injection_parameters is not None:
-            self.injection_parameters = self.convert_injection_parameters(
-                self.injection_parameters, extra_kwargs=self.extra_kwargs,
-                disable_convert=kwargs.get("disable_injection_conversion", False),
-                **kwargs.get(
-                    "injection_conversion_kwargs", {}
-                )
-            )
-        if self.priors is not None and len(self.priors):
-            if self.priors["samples"] != {}:
-                priors = self.priors["samples"]
-                self.priors["samples"] = self.convert_and_translate_prior_samples(
-                    priors, disable_convert=kwargs.get(
-                        "disable_prior_conversion", False
-                    ), **kwargs.get("prior_conversion_kwargs", {})
-                )
 
-    def convert_and_translate_prior_samples(
-        self, priors, disable_convert=False, **kwargs
-    ):
-        """
+    def _convert_samples(self, parameters, samples, **kwargs):
+        """Convert a set of posterior samples via the conversion module
+
+        Parameters
+        ----------
+        parameters: list
+            list of parameter names
+        samples: 2d list
+            2d list of samples where the columns correspond to the posterior
+            samples for parameters
+        **kwargs: dict
+            all kwargs passed to the conversion module
         """
-        default_parameters = list(priors.keys())
-        default_samples = [
-            [priors[parameter][i] for parameter in default_parameters] for i
-            in range(len(priors[default_parameters[0]]))
-        ]
-        parameters, samples = self.translate_parameters(
-            default_parameters, default_samples
-        )
-        if not disable_convert:
-            return convert(
-                parameters, samples, extra_kwargs=self.extra_kwargs, **kwargs
-            )
-        return SamplesDict(parameters, samples)
+        from pesummary.gw.conversions import convert
+
+        if "no_conversion" in kwargs.keys():
+            no_conversion = kwargs.pop("no_conversion")
+        else:
+            no_conversion = False
+        if not no_conversion:
+            data = convert(parameters, samples, **kwargs)
+            return data
+        return
 
     def write(self, package="core", **kwargs):
         """Save the data to file
@@ -270,6 +272,79 @@ class GWRead(Read):
         """
         pass
 
+    def generate_all_prior_samples(self, priors, extra_kwargs, **kwargs):
+        """Generate all prior samples via the conversion module
+
+        Parameters
+        ----------
+        **kwargs: dict
+            all kwargs passed to the conversion module
+        """
+        default_parameters = list(priors.keys())
+        default_samples = np.array(
+            [priors[key] for key in default_parameters]
+        ).T.tolist()
+        parameters, samples = self.translate_parameters(
+            default_parameters, default_samples
+        )
+        if "disable_prior_conversion" in kwargs.keys():
+            kwargs["no_conversion"] = kwargs.get(
+                "disable_prior_conversion"
+            )
+        if kwargs.get("no_conversion", False):
+            return SamplesDict(parameters, samples)
+        data = self._convert(
+            parameters, samples, extra_kwargs=extra_kwargs,
+            **kwargs
+        )
+        return data
+
+    def generate_all_posterior_samples(
+        self, parameters, samples, extra_kwargs, **kwargs
+    ):
+        """Generate all posterior samples via the conversion module
+
+        Parameters
+        ----------
+        **kwargs: dict
+            all kwargs passed to the conversion module
+        """
+        kwargs.update({"return_dict": False})
+        data = self._convert_samples(
+            parameters, samples, extra_kwargs=extra_kwargs, **kwargs
+        )
+        return data
+
+    def convert(self, quantity, **kwargs):
+        """Convert the stored samples
+
+        Parameters
+        ----------
+        quantity: str
+            The quantity you wish to convert. This can be 'posterior', 'prior',
+            'injection' or 'all'
+        **kwargs: dict
+            all kwargs passed to the conversion module
+        """
+        if quantity.lower() == "posterior":
+            logger.info("Converting the posterior samples")
+            self.generate_all_posterior_samples(**kwargs)
+        elif quantity.lower() == "prior":
+            logger.info("Converting the prior samples")
+            self.generate_all_prior_samples(**kwargs)
+        elif quantity.lower() == "injection":
+            logger.info("Converting the injection samples")
+            self.generate_all_injection_samples(**kwargs)
+        elif quantity.lower() == "all":
+            for _quantity in ["posterior", "prior", "injection"]:
+                self.convert(_quantity, **kwargs)
+        else:
+            raise ValueError(
+                "Unrecognised quantity '{}'. Please select either "
+                "'posterior', 'prior', 'injection' or 'all'".format(quantity)
+            )
+        return
+
     @staticmethod
     def check_for_calibration_data(function, path_to_results_file):
         """Check to see if there is any calibration data in the results file
@@ -539,6 +614,12 @@ class GWSingleAnalysisRead(GWRead, SingleAnalysisRead):
     generate_all_posterior_samples:
         generate all posterior distributions that may be derived from
         sampled distributions
+    generate_all_prior_samples:
+        generate all prior distributions that may be derived from the
+        stored prior distributions
+    generate_all_injection_samples:
+        generate all injection values that may be derived from the stored
+        injection values
     """
     def __init__(self, *args, **kwargs):
         super(GWSingleAnalysisRead, self).__init__(*args, **kwargs)
@@ -568,6 +649,23 @@ class GWSingleAnalysisRead(GWRead, SingleAnalysisRead):
         """
         return _add_log_likelihood(parameters, samples)
 
+    def generate_all_prior_samples(self, **kwargs):
+        """Generate all prior samples via the conversion module
+
+        Parameters
+        ----------
+        **kwargs: dict
+            all kwargs passed to the conversion module
+        """
+        if self.priors is not None and len(self.priors):
+            if self.priors["samples"] != {}:
+                data = super(GWSingleAnalysisRead, self).generate_all_prior_samples(
+                    self.priors["samples"], self.extra_kwargs, **kwargs
+                )
+                if data is not None:
+                    self.priors["samples"] = data
+        return
+
     def generate_all_posterior_samples(self, **kwargs):
         """Generate all posterior samples via the conversion module
 
@@ -576,43 +674,32 @@ class GWSingleAnalysisRead(GWRead, SingleAnalysisRead):
         **kwargs: dict
             all kwargs passed to the conversion module
         """
-        if "no_conversion" in kwargs.keys():
-            no_conversion = kwargs.pop("no_conversion")
-        else:
-            no_conversion = False
-        if not no_conversion:
-            from pesummary.gw.conversions import convert
-
-            data = convert(
-                self.parameters, self.samples, extra_kwargs=self.extra_kwargs,
-                return_dict=False, **kwargs
-            )
+        data = super(GWSingleAnalysisRead, self).generate_all_posterior_samples(
+            self.parameters, self.samples, self.extra_kwargs, **kwargs
+        )
+        if data is not None:
             self.parameters = data[0]
             self.converted_parameters = self.parameters.added
             self.samples = data[1]
             if kwargs.get("return_kwargs", False):
                 self.extra_kwargs = data[2]
 
-    def convert_injection_parameters(
-        self, data, extra_kwargs={"sampler": {}, "meta_data": {}},
-        disable_convert=False, **kwargs
-    ):
-        """Apply the conversion module to the injection data
+    def generate_all_injection_samples(self, **kwargs):
+        """Generate all injection samples via the conversion module
 
         Parameters
         ----------
-        data: dict
-            dictionary of injection data keyed by the parameter
-        extra_kwargs: dict, optional
-            optional kwargs to pass to the conversion module
-        disable_convert: Bool, optional
-            if True, do not convert injection parameters
-        **kwargs: dict, optional
-            all kwargs passed to the pesummary.gw.conversions.convert function
+        **kwargs: dict
+            all kwargs passed to the conversion module
         """
-        return convert_injection_parameters(
-            data, extra_kwargs=extra_kwargs, disable_convert=disable_convert,
-            sampled_parameters=self.parameters, **kwargs
+        if "disable_injection_conversion" in kwargs.keys():
+            kwargs["no_conversion"] = kwargs.get(
+                "disable_injection_conversion"
+            )
+        self.injection_parameters = convert_injection_parameters(
+            self.injection_parameters, extra_kwargs=self.extra_kwargs,
+            disable_convert=kwargs.get("no_conversion", False),
+            **kwargs
         )
 
     def to_lalinference(self, **kwargs):
@@ -687,31 +774,6 @@ class GWMultiAnalysisRead(GWRead, MultiAnalysisRead):
             except (KeyError, AttributeError):
                 self.skymap = self.data["skymap"]
 
-    def convert_and_translate_prior_samples(self, priors, disable_convert=False):
-        """
-        """
-        from pesummary.utils.samples_dict import MultiAnalysisSamplesDict
-
-        mydict = {}
-        for num, label in enumerate(self.labels):
-            if label in priors.keys() and len(priors[label]):
-                default_parameters = list(priors[label].keys())
-                default_samples = np.array(
-                    [priors[label][_param] for _param in default_parameters]
-                ).T
-                parameters, samples = self.translate_parameters(
-                    [default_parameters], [default_samples]
-                )
-                if not disable_convert:
-                    mydict[label] = convert(
-                        parameters[0], samples[0], extra_kwargs=self.extra_kwargs[num]
-                    )
-                else:
-                    mydict[label] = SamplesDict(parameters[0], samples[0])
-            else:
-                mydict[label] = {}
-        return MultiAnalysisSamplesDict(mydict)
-
     def check_for_log_likelihood(self, parameters):
         if all("log_likelihood" in p for p in parameters):
             return True
@@ -745,14 +807,52 @@ class GWMultiAnalysisRead(GWRead, MultiAnalysisRead):
             samples_logl.append(ss)
         return parameters_logl, samples_logl
 
+    def generate_all_prior_samples(self, labels=None, **kwargs):
+        """Apply the conversion module to the prior samples
+
+        Parameters
+        ----------
+        labels: list, optional
+            list of analyses to consider
+        **kwargs: dict
+            all kwargs passed to the conversion module
+        """
+        from pesummary.utils.samples_dict import MultiAnalysisSamplesDict
+
+        mydict = {}
+        for num, label in enumerate(self.labels):
+            _kwargs = kwargs.copy()
+            if labels is not None and label not in labels:
+                _kwargs["no_conversion"] = True
+                if label not in self.priors.keys() or not len(self.priors[label]):
+                    mydict[label] = {}
+                    continue
+                mydict[label] = (
+                    super(GWMultiAnalysisRead, self).generate_all_prior_samples(
+                        self.priors[label]["samples"], self.extra_kwargs[num],
+                        **_kwargs
+                    )
+                )
+            elif label in self.priors.keys() and len(self.priors[label]):
+                mydict[label] = (
+                    super(GWMultiAnalysisRead, self).generate_all_prior_samples(
+                        self.priors[label]["samples"], self.extra_kwargs[num],
+                        **kwargs
+                    )
+                )
+            else:
+                mydict[label] = {}
+        return MultiAnalysisSamplesDict(mydict)
+
     def generate_all_posterior_samples(self, labels=None, **conversion_kwargs):
+        """Apply the conversion module to the posterior distributions
+        """
         if "no_conversion" in conversion_kwargs.keys():
             no_conversion = conversion_kwargs.pop("no_conversion")
         else:
             no_conversion = False
         if no_conversion:
             return
-        from pesummary.gw.conversions import convert
 
         converted_params, converted_samples, converted_kwargs = [], [], []
         _converted_params = []
@@ -773,9 +873,8 @@ class GWMultiAnalysisRead(GWRead, MultiAnalysisRead):
             if _conversion_kwargs.get("evolve_spins", False):
                 if not _conversion_kwargs.get("return_kwargs", False):
                     _conversion_kwargs["return_kwargs"] = True
-            data = convert(
-                param, samples, extra_kwargs=kwargs, return_dict=False,
-                **_conversion_kwargs
+            data = super(GWMultiAnalysisRead, self).generate_all_posterior_samples(
+                param, samples, kwargs, **_conversion_kwargs
             )
             converted_params.append(data[0])
             _converted_params.append(data[0].added)
@@ -792,22 +891,34 @@ class GWMultiAnalysisRead(GWRead, MultiAnalysisRead):
                 )
             }
 
-    def convert_injection_parameters(
-        self, data, extra_kwargs={"sampler": {}, "meta_data": {}},
-        disable_convert=False
-    ):
+    def generate_all_injection_samples(self, labels=None, **kwargs):
         """Apply the conversion module to the injection data
+
+        Parameters
+        ----------
+        labels: list, optional
+            list of analyses to consider
+        **kwargs: dict
+            all kwargs passed to the conversion module
         """
+        if "disable_injection_conversion" in kwargs.keys():
+            kwargs["no_conversion"] = kwargs.get(
+                "disable_injection_conversion"
+            )
+        data = self.injection_parameters
         for num, label in enumerate(self.labels):
+            _kwargs = kwargs.copy()
+            if labels is not None and label not in labels:
+                _kwargs["no_conversion"] = True
             _identifier = label
-            if isinstance(data, dict):
-                _data = data[label]
+            if isinstance(self.injection_parameters, dict):
+                _data = self.injection_parameters[label]
             else:
-                _data = data[num]
+                _data = self.injection_parameters[num]
                 _identifier = num
             data[_identifier] = convert_injection_parameters(
-                _data, extra_kwargs=extra_kwargs[num],
-                disable_convert=disable_convert,
+                _data, extra_kwargs=self.extra_kwargs[num],
+                disable_convert=_kwargs.get("no_conversion"),
                 sampled_parameters=self.parameters[num]
             )
-        return data
+        self.injection_parameters = data
diff --git a/pesummary/gw/file/formats/bilby.py b/pesummary/gw/file/formats/bilby.py
index f4fc3105..7bd70c14 100644
--- a/pesummary/gw/file/formats/bilby.py
+++ b/pesummary/gw/file/formats/bilby.py
@@ -128,6 +128,15 @@ class Bilby(GWSingleAnalysisRead):
     generate_all_posterior_samples:
         generate all posterior distributions that may be derived from
         sampled distributions
+    generate_all_prior_samples:
+        generate all prior distributions that may be derived from the
+        stored prior distributions
+    generate_all_injection_samples:
+        generate all injection values that may be derived from the stored
+        injection values
+    convert:
+        convert either the posterior distributions, prior distribution and/or
+        the injection samples.
     """
     def __init__(self, path_to_results_file, **kwargs):
         super(Bilby, self).__init__(path_to_results_file, **kwargs)
diff --git a/pesummary/gw/file/formats/default.py b/pesummary/gw/file/formats/default.py
index 841b5654..378260d6 100644
--- a/pesummary/gw/file/formats/default.py
+++ b/pesummary/gw/file/formats/default.py
@@ -53,6 +53,15 @@ class SingleAnalysisDefault(GWSingleAnalysisRead):
     generate_all_posterior_samples:
         generate all posterior distributions that may be derived from
         sampled distributions
+    generate_all_prior_samples:
+        generate all prior distributions that may be derived from the
+        stored prior distributions
+    generate_all_injection_samples:
+        generate all injection values that may be derived from the stored
+        injection values
+    convert:
+        convert either the posterior distributions, prior distribution and/or
+        the injection samples.
     """
     def __init__(self, *args, _data=None, **kwargs):
         super(SingleAnalysisDefault, self).__init__(*args, **kwargs)
@@ -96,6 +105,15 @@ class MultiAnalysisDefault(GWMultiAnalysisRead):
     generate_all_posterior_samples:
         generate all posterior distributions that may be derived from
         sampled distributions
+    generate_all_prior_samples:
+        generate all prior distributions that may be derived from the
+        stored prior distributions
+    generate_all_injection_samples:
+        generate all injection values that may be derived from the stored
+        injection values
+    convert:
+        convert either the posterior distributions, prior distribution and/or
+        the injection samples.
     """
     def __init__(self, *args, _data=None, **kwargs):
         super(MultiAnalysisDefault, self).__init__(*args, **kwargs)
@@ -141,6 +159,12 @@ class Default(CoreDefault):
     generate_all_posterior_samples:
         generate all posterior distributions that may be derived from
         sampled distributions
+    generate_all_prior_samples:
+        generate all prior distributions that may be derived from the
+        stored prior distributions
+    generate_all_injection_samples:
+        generate all injection values that may be derived from the stored
+        injection values
     """
     def load_map(self):
         _load_map = super(Default, self).load_map(self)
diff --git a/pesummary/gw/file/formats/lalinference.py b/pesummary/gw/file/formats/lalinference.py
index 65df1a00..47f8b80b 100644
--- a/pesummary/gw/file/formats/lalinference.py
+++ b/pesummary/gw/file/formats/lalinference.py
@@ -126,6 +126,15 @@ class LALInference(GWSingleAnalysisRead):
     generate_all_posterior_samples:
         generate all posterior distributions that may be derived from
         sampled distributions
+    generate_all_prior_samples:
+        generate all prior distributions that may be derived from the
+        stored prior distributions
+    generate_all_injection_samples:
+        generate all injection values that may be derived from the stored
+        injection values
+    convert:
+        convert either the posterior distributions, prior distribution and/or
+        the injection samples.
     """
     def __init__(self, path_to_results_file, injection_file=None, **kwargs):
         super(LALInference, self).__init__(path_to_results_file, **kwargs)
diff --git a/pesummary/gw/file/formats/pesummary.py b/pesummary/gw/file/formats/pesummary.py
index c47e2852..c6f7198c 100644
--- a/pesummary/gw/file/formats/pesummary.py
+++ b/pesummary/gw/file/formats/pesummary.py
@@ -108,6 +108,15 @@ class PESummary(GWMultiAnalysisRead, CorePESummary):
     generate_all_posterior_samples:
         generate all posterior distributions that may be derived from
         sampled distributions
+    generate_all_prior_samples:
+        generate all prior distributions that may be derived from the
+        stored prior distributions
+    generate_all_injection_samples:
+        generate all injection values that may be derived from the stored
+        injection values
+    convert:
+        convert either the posterior distributions, prior distribution and/or
+        the injection samples.
     """
     def __init__(self, path_to_results_file, **kwargs):
         super(PESummary, self).__init__(
-- 
GitLab


From d87fe4ee7270d5df693e87f40595173f5c156ebc Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Fri, 30 Apr 2021 13:30:31 +0100
Subject: [PATCH 08/13] call the convert method rather than
 generate_all_posterior_samples

---
 pesummary/core/file/formats/base_read.py |  5 +++++
 pesummary/core/inputs.py                 |  4 ++--
 pesummary/utils/samples_dict.py          | 18 ++++++++++++++++++
 3 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/pesummary/core/file/formats/base_read.py b/pesummary/core/file/formats/base_read.py
index 43f209b1..6322d728 100644
--- a/pesummary/core/file/formats/base_read.py
+++ b/pesummary/core/file/formats/base_read.py
@@ -317,6 +317,11 @@ class Read(object):
                 "Unable to find a posterior samples table in '{}'".format(path)
             )
 
+    def convert(self, *args, **kwargs):
+        """Empty function
+        """
+        pass
+
     def generate_all_posterior_samples(self, **kwargs):
         """Empty function
         """
diff --git a/pesummary/core/inputs.py b/pesummary/core/inputs.py
index 1b8f06b4..18586c4f 100644
--- a/pesummary/core/inputs.py
+++ b/pesummary/core/inputs.py
@@ -126,7 +126,7 @@ class _Input(object):
             labels = compare
 
         if not f.mcmc_samples:
-            f.generate_all_posterior_samples(labels=labels, **kwargs)
+            f.convert(labels=labels, **kwargs)
 
         parameters = f.parameters
         if not f.mcmc_samples:
@@ -253,7 +253,7 @@ class _Input(object):
 
         if nsamples is not None:
             f.downsample(nsamples)
-        f.generate_all_posterior_samples(**kwargs)
+        f.convert(**kwargs)
         if injection:
             f.add_injection_parameters_from_file(
                 injection, conversion_kwargs=kwargs
diff --git a/pesummary/utils/samples_dict.py b/pesummary/utils/samples_dict.py
index 468f41be..8e787c7d 100644
--- a/pesummary/utils/samples_dict.py
+++ b/pesummary/utils/samples_dict.py
@@ -72,6 +72,9 @@ class SamplesDict(Dict):
         Remove the first N samples from each distribution
     plot:
         Generate a plot based on the posterior samples stored
+    convert:
+        Convert the posterior samples in the SamplesDict object according to
+        a conversion function
     generate_all_posterior_samples:
         Convert the posterior samples in the SamplesDict object according to
         a conversion function
@@ -393,6 +396,21 @@ class SamplesDict(Dict):
         """
         return super(SamplesDict, self).plot(*args, type=type, **kwargs)
 
+    def convert(self, function=None, **kwargs):
+        """Convert samples stored in the SamplesDict according to a conversion
+        function
+
+        Parameters
+        ----------
+        function: func, optional
+            function to use when converting posterior samples. Must take a
+            dictionary as input and return a dictionary of converted posterior
+            samples. Default `pesummary.gw.conversions.convert
+        **kwargs: dict, optional
+            All additional kwargs passed to function
+        """
+        return self.generate_all_posterior_samples(function=function, **kwargs)
+
     def generate_all_posterior_samples(self, function=None, **kwargs):
         """Convert samples stored in the SamplesDict according to a conversion
         function
-- 
GitLab


From 2936db3bf1b1732e0993d19cd7a42f61f67712dc Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Fri, 30 Apr 2021 14:03:35 +0100
Subject: [PATCH 09/13] pass quantity

---
 pesummary/core/inputs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pesummary/core/inputs.py b/pesummary/core/inputs.py
index 18586c4f..c5bef65d 100644
--- a/pesummary/core/inputs.py
+++ b/pesummary/core/inputs.py
@@ -126,7 +126,7 @@ class _Input(object):
             labels = compare
 
         if not f.mcmc_samples:
-            f.convert(labels=labels, **kwargs)
+            f.convert("all", labels=labels, **kwargs)
 
         parameters = f.parameters
         if not f.mcmc_samples:
@@ -253,7 +253,7 @@ class _Input(object):
 
         if nsamples is not None:
             f.downsample(nsamples)
-        f.convert(**kwargs)
+        f.convert("all", **kwargs)
         if injection:
             f.add_injection_parameters_from_file(
                 injection, conversion_kwargs=kwargs
-- 
GitLab


From ff6740cb1500fa64893f411dbd4216622d79b710 Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Fri, 30 Apr 2021 20:42:26 +0100
Subject: [PATCH 10/13] typo

---
 pesummary/gw/file/formats/base_read.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pesummary/gw/file/formats/base_read.py b/pesummary/gw/file/formats/base_read.py
index 239cc303..00e8d238 100644
--- a/pesummary/gw/file/formats/base_read.py
+++ b/pesummary/gw/file/formats/base_read.py
@@ -213,7 +213,7 @@ class GWRead(Read):
         )
         super(GWRead, self).load(function, _data=data, **kwargs)
 
-    def _convert_samples(self, parameters, samples, **kwargs):
+    def _convert(self, parameters, samples, **kwargs):
         """Convert a set of posterior samples via the conversion module
 
         Parameters
@@ -310,7 +310,7 @@ class GWRead(Read):
             all kwargs passed to the conversion module
         """
         kwargs.update({"return_dict": False})
-        data = self._convert_samples(
+        data = self._convert(
             parameters, samples, extra_kwargs=extra_kwargs, **kwargs
         )
         return data
-- 
GitLab


From 5c1f3d73942ca8c73f270e9c48c1814567244be0 Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Mon, 3 May 2021 16:46:58 +0100
Subject: [PATCH 11/13] typo

---
 pesummary/gw/file/formats/base_read.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pesummary/gw/file/formats/base_read.py b/pesummary/gw/file/formats/base_read.py
index 00e8d238..bae2cf27 100644
--- a/pesummary/gw/file/formats/base_read.py
+++ b/pesummary/gw/file/formats/base_read.py
@@ -696,6 +696,8 @@ class GWSingleAnalysisRead(GWRead, SingleAnalysisRead):
             kwargs["no_conversion"] = kwargs.get(
                 "disable_injection_conversion"
             )
+        if self.injection_parameters is None:
+            return
         self.injection_parameters = convert_injection_parameters(
             self.injection_parameters, extra_kwargs=self.extra_kwargs,
             disable_convert=kwargs.get("no_conversion", False),
@@ -916,6 +918,8 @@ class GWMultiAnalysisRead(GWRead, MultiAnalysisRead):
             else:
                 _data = self.injection_parameters[num]
                 _identifier = num
+            if _data is None:
+                continue
             data[_identifier] = convert_injection_parameters(
                 _data, extra_kwargs=self.extra_kwargs[num],
                 disable_convert=_kwargs.get("no_conversion"),
-- 
GitLab


From d8dd407798b68482c2df3a9f05767303e045106a Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Tue, 8 Jun 2021 17:06:36 +0100
Subject: [PATCH 12/13] do not return kwargs for priors and injections

---
 pesummary/gw/file/formats/base_read.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pesummary/gw/file/formats/base_read.py b/pesummary/gw/file/formats/base_read.py
index bae2cf27..c6bd8c3d 100644
--- a/pesummary/gw/file/formats/base_read.py
+++ b/pesummary/gw/file/formats/base_read.py
@@ -119,6 +119,7 @@ def convert_injection_parameters(
     for i in nan_inds[::-1]:
         parameters.remove(parameters[i])
         samples[0].remove(samples[0][i])
+    kwargs["return_kwargs"] = False
     inj_samples = convert(
         parameters, samples, extra_kwargs=extra_kwargs, **kwargs
     )
@@ -291,6 +292,7 @@ class GWRead(Read):
             kwargs["no_conversion"] = kwargs.get(
                 "disable_prior_conversion"
             )
+        kwargs["return_kwargs"] = False
         if kwargs.get("no_conversion", False):
             return SamplesDict(parameters, samples)
         data = self._convert(
-- 
GitLab


From 00a9527d098bcbdab86bfe803a18f5d441d9b688 Mon Sep 17 00:00:00 2001
From: Charlie Hoy <hoyc1@cardiff.ac.uk>
Date: Tue, 8 Jun 2021 18:36:37 +0100
Subject: [PATCH 13/13] typo

---
 pesummary/gw/file/formats/base_read.py | 5 +++++
 pesummary/gw/file/formats/bilby.py     | 3 +++
 pesummary/tests/read_test.py           | 2 ++
 3 files changed, 10 insertions(+)

diff --git a/pesummary/gw/file/formats/base_read.py b/pesummary/gw/file/formats/base_read.py
index c6bd8c3d..5176d664 100644
--- a/pesummary/gw/file/formats/base_read.py
+++ b/pesummary/gw/file/formats/base_read.py
@@ -292,6 +292,11 @@ class GWRead(Read):
             kwargs["no_conversion"] = kwargs.get(
                 "disable_prior_conversion"
             )
+        if hasattr(self, "disable_prior_conversion"):
+            if self.disable_prior_conversion:
+                kwargs["no_conversion"] = kwargs.get(
+                    "disable_prior_conversion"
+                )
         kwargs["return_kwargs"] = False
         if kwargs.get("no_conversion", False):
             return SamplesDict(parameters, samples)
diff --git a/pesummary/gw/file/formats/bilby.py b/pesummary/gw/file/formats/bilby.py
index 7bd70c14..b3aca423 100644
--- a/pesummary/gw/file/formats/bilby.py
+++ b/pesummary/gw/file/formats/bilby.py
@@ -141,6 +141,9 @@ class Bilby(GWSingleAnalysisRead):
     def __init__(self, path_to_results_file, **kwargs):
         super(Bilby, self).__init__(path_to_results_file, **kwargs)
         self.load(self._grab_data_from_bilby_file, **kwargs)
+        self.disable_prior_conversion = kwargs.get(
+            "disable_prior_conversion", False
+        )
 
     @staticmethod
     def grab_priors(bilby_object, nsamples=5000):
diff --git a/pesummary/tests/read_test.py b/pesummary/tests/read_test.py
index c9329aa5..fe028d5f 100644
--- a/pesummary/tests/read_test.py
+++ b/pesummary/tests/read_test.py
@@ -1555,8 +1555,10 @@ class TestGWJsonBilbyFile(GWBaseRead):
         assert "final_mass_source_non_evolved" not in self.result.parameters
         for param, prior in self.result.priors["samples"].items():
             assert isinstance(prior, np.ndarray)
+        self.result.generate_all_prior_samples()
         assert "final_mass_source_non_evolved" in self.result.priors["samples"].keys()
         f = read_function(self.path, disable_prior_conversion=True)
+        self.result.generate_all_prior_samples()
         assert "final_mass_source_non_evolved" not in f.priors["samples"].keys()
         f = read_function(self.path, disable_prior_sampling=True)
         assert not len(f.priors["samples"])
-- 
GitLab