Analysing the results
At the end of the run, Lensed will output a summary of the statistics and a table for the parameter values. The table columns give the individual marginal mean values, standard deviations (sigma), maximum likelihood (ML) and maximum a posteriori (MAP) parameters.
summary log-evidence: -5123.3227 ± 0.4202 max log-like: -5061.6840 min chi²/dof: 1.0136 parameters parameter mean sigma ML MAP ---------------------------------------------------------- x_L 50.5049 0.0118 50.5107 50.5001 y_L 50.4907 0.0118 50.4901 50.5116 r_L 17.4325 0.0062 17.4299 17.4340 q_L 0.7491 0.0016 0.7487 0.7518 \theta_L 45.0175 0.0821 44.9905 44.9403 x_S 49.0356 0.0082 49.0414 49.0461 y_S 51.7509 0.0074 51.7502 51.7606 r_S 3.8515 0.1866 3.8357 3.8413 mag_S -3.0694 0.0365 -3.0691 -3.0547 n_S 3.1509 0.0818 3.1441 3.1506 q_S 0.8921 0.0135 0.8868 0.8795 \theta_S 31.4591 4.0208 31.0952 28.3584
This table is meant to provide a quick overview of the results, but often does not tell the whole story of the parameter space. Lensed can further provide a number of output files which contain the full posterior distribution. These files can be analysed with statistical tools from third parties, such as GetDist.
The posterior distribution
A number of output files for the posterior distribution are created when Lensed
runs with the
output = true configuration option:
<root>.txt: The chains file, compatible with GetDist. Each row contains one sample from the posterior. The (2 + number of parameters) columns contain the sample probability, -2*loglikehood, and parameter values. The sample probability is the sample prior mass multiplied by the likelihood, and normalized by the evidence.
<root>post_equal_weights.dat: This file contains equally weighted samples from the posterior. Each row is thus a randomly drawn sample from the posterior distribution. The columns are the parameter values, followed by their likelihood value.
<root>stats.dat: This file contains a human-readable summary of the posterior distribution. Contains the log-evidence, parameter mean values and standard deviations, together with their maximum likelihood and maximum a posteriori. If there are multiple modes, the statistics are given globally and for each of the individual modes.
<root>post_separate.dat: This file is only created if the posterior is multi-model. It contains the posterior samples for each mode, separated by 2 blank lines. The format is the same as for the
<root>summary.txt: This file contains (number of modes + 1) rows. The first row contains the global statistics for the posterior. Each subsequent row is a single mode, with the following (number of parameters * 4 + 2) values: mean, standard deviation, maximum likelihood, and maximum a posteriori for each parameter, together with the local log-evidence and maximum log-likelihood values of the mode. If importance nested sampling is used, the first row contains the INS log-evidence estimate at the end.
Analysis with GetDist
GetDist is a tool for analysing and plotting posterior distributions obtained from MCMC chains. It was written by Antony Lewis and turned into a standalone Python package, after being part of the CosmoMC suite.
Installing GetDist is straightforward using the Python package manager
$ pip install GetDist
Once GetDist is installed, it can be used to analyse the output of Lensed right away. The syntax is
$ GetDist.py [paramfile] [root]
where either the
[paramfile] or the
[root] can be omitted. If no parameter
file is given, default values are used. If no root is given, it must have been
specified in the parameter file.
A sample parameter file for GetDist is available at
extras/getdist.ini in the
Lensed root directory. It contains sensible defaults for analysing the results
of Lensed. Using this file, one of the provided examples can be analysed (from
examples folder) using
examples$ GetDist.py ../extras/getdist.ini chains/test_sersic_bulge-
The output of the analysis can be found in the
Besides analysing the posterior and finding confidence intervals and summary
statistics, GetDist can be used to create scripts for plotting one-dimensional
marginal distributions, as well as two-, three-dimensional, and triangle plots
for the correlations between parameters. Note that GetDist does not create the
plots directly. It is necessary to run the Python files at
$ python plots/test_sersic_bulge-_tri.py
Below there are a number of sample plots from GetDist.
| Sample plots from GetDist | |-----------------------------------------------------------| | | | One-dimensional marginal distribution | | | | Two-dimensional correlations with confidence intervals | | | | Two-dimensional correlations | | | | Triangle plot |