From 619c1ae9887b35feea4441e82f7ab2f0d477d5f9 Mon Sep 17 00:00:00 2001
From: Gregory Ashton <gregory.ashton@ligo.org>
Date: Tue, 26 Feb 2019 21:04:04 -0800
Subject: [PATCH 1/2] Adds a results-file command line interface
---
cli_bilby/bilby_result.py | 78 +++++++++++++++++++++++++++++++++++++++
setup.py | 3 +-
2 files changed, 80 insertions(+), 1 deletion(-)
create mode 100644 cli_bilby/bilby_result.py
diff --git a/cli_bilby/bilby_result.py b/cli_bilby/bilby_result.py
new file mode 100644
index 000000000..419a190f2
--- /dev/null
+++ b/cli_bilby/bilby_result.py
@@ -0,0 +1,78 @@
+""" A command line interface to ease the process of batch jobs on result files
+
+Examples
+--------
+To convert all the JSON result files in `outdir` to hdf5 format:
+
+ $ bilby_result -r outdir/*json -c hdf5
+
+Note, by default this will save the new files in the outdir defined within the
+results files. To give a new location, use the `--outdir` argument.
+
+To print the version and `log_evidence` for all the result files in outdir:
+
+ $ bilby_result -r outdir/*json --print version log_evidence
+
+To generate a corner plot for all the files in outdir
+
+ $ bilby_result -r outdir/*json --call plot_corner
+
+This is effectively calling `plot_corner()` on each of the result files
+individually. Note that passing extra commands in is not yet implemented.
+
+"""
+import argparse
+import pandas as pd
+
+
+def setup_command_line_args():
+ parser = argparse.ArgumentParser(
+ description="Helper tool for bilby result files")
+ parser.add_argument("-r", "--results", nargs='+',
+ help="List of results files.")
+ parser.add_argument("-c", "--convert", type=str, choices=['json', 'hdf5'],
+ help="Convert all results.", default=False)
+ parser.add_argument("-o", "--outdir", type=str, default=None,
+ help="Output directory.")
+ parser.add_argument("-b", "--bayes", action='store_true',
+ help="Print all Bayes factors.")
+ parser.add_argument("-p", "--print", nargs='+', default=None,
+ help="Result dictionary keys to print.")
+ parser.add_argument("--call", nargs='+', default=None,
+ help="Result dictionary methods to call (no argument passing available).")
+ args, _ = parser.parse_known_args()
+
+ return args
+
+
+def print_bayes_factors(results):
+ print("\nPrinting Bayes factors:")
+ N = len(results)
+ for i, res in enumerate(results):
+ print("For label={}".format(res.label))
+ index = ['noise'] + [results[j].label for j in range(i + 1, N)]
+ data = [res.log_bayes_factor]
+ data += [res.log_evidence - results[j].log_evidence for j in range(i + 1, N)]
+ series = pd.Series(data=data, index=index, name=res.label)
+ print(series)
+
+
+def main():
+ args = setup_command_line_args()
+ import bilby
+ results = [bilby.core.result.read_in_result(filename=r)
+ for r in args.results]
+ if args.convert:
+ for r in results:
+ r.save_to_file(extension=args.convert, outdir=args.outdir)
+ if args.print is not None:
+ for r in results:
+ print("\nResult file: {}/{}".format(r.outdir, r.label))
+ for key in args.print:
+ print(" {}: {}".format(key, getattr(r, key, 'None')))
+ if args.call is not None:
+ for r in results:
+ for call in args.call:
+ getattr(r, call)()
+ if args.bayes:
+ print_bayes_factors(results)
diff --git a/setup.py b/setup.py
index 20f5e5577..441db8deb 100644
--- a/setup.py
+++ b/setup.py
@@ -85,7 +85,8 @@ setup(name='bilby',
'pandas',
'scipy'],
entry_points={'console_scripts':
- ['bilby_plot=cli_bilby.plot_multiple_posteriors:main']
+ ['bilby_plot=cli_bilby.plot_multiple_posteriors:main',
+ 'bilby_result=cli_bilby.bilby_result:main']
},
classifiers=[
"Programming Language :: Python :: 2.7",
--
GitLab
From 2f13912ccc0bad92285c2d66f422f05f12946adc Mon Sep 17 00:00:00 2001
From: Gregory Ashton <gregory.ashton@ligo.org>
Date: Fri, 1 Mar 2019 10:25:58 +1100
Subject: [PATCH 2/2] Fix formatting issues and add --ipython option
---
cli_bilby/bilby_result.py | 49 ++++++++++++++++++++++++++++-----------
1 file changed, 35 insertions(+), 14 deletions(-)
diff --git a/cli_bilby/bilby_result.py b/cli_bilby/bilby_result.py
index 419a190f2..aa0ea0f18 100644
--- a/cli_bilby/bilby_result.py
+++ b/cli_bilby/bilby_result.py
@@ -24,11 +24,14 @@ individually. Note that passing extra commands in is not yet implemented.
import argparse
import pandas as pd
+import bilby
+
def setup_command_line_args():
parser = argparse.ArgumentParser(
- description="Helper tool for bilby result files")
- parser.add_argument("-r", "--results", nargs='+',
+ description="Helper tool for bilby result files",
+ epilog=print(__doc__))
+ parser.add_argument("-r", "--results", nargs='+', required=True,
help="List of results files.")
parser.add_argument("-c", "--convert", type=str, choices=['json', 'hdf5'],
help="Convert all results.", default=False)
@@ -40,39 +43,57 @@ def setup_command_line_args():
help="Result dictionary keys to print.")
parser.add_argument("--call", nargs='+', default=None,
help="Result dictionary methods to call (no argument passing available).")
+ parser.add_argument("--ipython", action='store_true',
+ help=("For each result given, drops the user into an "
+ "IPython shell with the result loaded in"))
args, _ = parser.parse_known_args()
return args
-def print_bayes_factors(results):
+def read_in_results(filename_list):
+ results_list = []
+ for filename in filename_list:
+ results_list.append(bilby.core.result.read_in_result(filename=filename))
+ return results_list
+
+
+def print_bayes_factors(results_list):
print("\nPrinting Bayes factors:")
- N = len(results)
- for i, res in enumerate(results):
+ N = len(results_list)
+ for i, res in enumerate(results_list):
print("For label={}".format(res.label))
- index = ['noise'] + [results[j].label for j in range(i + 1, N)]
+ index = ['noise'] + [results_list[j].label for j in range(i + 1, N)]
data = [res.log_bayes_factor]
- data += [res.log_evidence - results[j].log_evidence for j in range(i + 1, N)]
+ data += [res.log_evidence - results_list[j].log_evidence for j in range(i + 1, N)]
series = pd.Series(data=data, index=index, name=res.label)
print(series)
+def drop_to_ipython(results_list):
+ for result in results_list:
+ message = "Opened IPython terminal for result {}".format(result.label)
+ message += "\nBilby result loaded as `result`"
+ import IPython
+ IPython.embed(header=message)
+
+
def main():
args = setup_command_line_args()
- import bilby
- results = [bilby.core.result.read_in_result(filename=r)
- for r in args.results]
+ results_list = read_in_results(args.results)
if args.convert:
- for r in results:
+ for r in results_list:
r.save_to_file(extension=args.convert, outdir=args.outdir)
if args.print is not None:
- for r in results:
+ for r in results_list:
print("\nResult file: {}/{}".format(r.outdir, r.label))
for key in args.print:
print(" {}: {}".format(key, getattr(r, key, 'None')))
if args.call is not None:
- for r in results:
+ for r in results_list:
for call in args.call:
getattr(r, call)()
if args.bayes:
- print_bayes_factors(results)
+ print_bayes_factors(results_list)
+ if args.ipython:
+ drop_to_ipython(results_list)
--
GitLab