autofit.Emcee

class Emcee

Bases: AbstractMCMC

An Emcee non-linear search.

For a full description of Emcee, checkout its Github and readthedocs webpages:

https://github.com/dfm/emcee

https://emcee.readthedocs.io/en/stable/

If you use Emcee as part of a published work, please cite the package following the instructions under the Attribution section of the GitHub page.

Parameters:

• name (Optional[str]) – The name of the search, controlling the last folder results are output.

• path_prefix (Optional[str]) – The path of folders prefixing the name folder where results are output.

• unique_tag (Optional[str]) – The name of a unique tag for this model-fit, which will be given a unique entry in the sqlite database and also acts as the folder after the path prefix and before the search name.

• initializer (Optional[Initializer]) – Generates the initialize samples of non-linear parameter space (see autofit.non_linear.initializer).

• auto_correlation_settings – Customizes and performs auto correlation calculations performed during and after the search.

• number_of_cores (Optional[int]) – The number of cores sampling is performed using a Python multiprocessing Pool instance.

• session (Optional[Session]) – An SQLalchemy session instance so the results of the model-fit are written to an SQLite database.

Methods

auto_correlations_from
check_model
config_dict_test_mode_from	Returns a configuration dictionary for test mode meaning that the sampler terminates as quickly as possible.
copy_with_paths
exact_fit	rtype: Tuple[MeanField, Status]
fit	Fit a model, M with some function f that takes instances of the class represented by model M and gives a score for their fitness.
fit_sequential	Fit multiple analyses contained within the analysis sequentially.
make_pool	Make the pool instance used to parallelize a NonLinearSearch alongside a set of unique ids for every process in the pool.
make_sneakier_pool	rtype: SneakierPool
make_sneaky_pool	Create a pool for multiprocessing that uses slight-of-hand to avoid copying the fitness function between processes multiple times.
optimise	Perform optimisation for expectation propagation.
output_search_internal	Output the sampler results to hard-disk in their internal format.
perform_update	Perform an update of the non-linear search's model-fitting results.
perform_visualization	Perform visualization of the non-linear search's model-fitting results.
plot_results
post_fit_output	Cleans up the output folderds after a completed non-linear search.
pre_fit_output	Outputs attributes of fit before the non-linear search begins.
remove_state_files
result_via_completed_fit	Returns the result of the non-linear search of a completed model-fit.
samples_from	Loads the samples of a non-linear search from its output files.
samples_info_from
samples_via_csv_from	Returns a Samples object from the samples.csv and samples_info.json files.
samples_via_internal_from	Returns a Samples object from the emcee internal results.
start_resume_fit	Start a non-linear search from scratch, or resumes one which was previously terminated mid-way through.

Attributes

backend	The Emcee hdf5 backend, which provides access to all samples, likelihoods, etc.
backend_filename
config_dict_run	A property that is only computed once per instance and then replaces itself with an ordinary attribute.
config_dict_search	A property that is only computed once per instance and then replaces itself with an ordinary attribute.
config_dict_settings	rtype: Dict
config_type
logger	Log 'msg % args' with severity 'DEBUG'.
name
paths	rtype: Optional[AbstractPaths]
plotter_cls
samples_cls
timer	Returns the timer of the search, which is used to output informaiton such as how long the search took and how much parallelization sped up the search time.
using_mpi	Whether the search is being performing using MPI for parallelisation or not.

output_search_internal(search_internal)

Output the sampler results to hard-disk in their internal format.

Emcee uses a backend to store and load results, therefore the outputting of the search internal to a dill file is disabled.

Parameters:

sampler – The nautilus sampler object containing the results of the model-fit.

samples_via_internal_from(model, search_internal=None)

Returns a Samples object from the emcee internal results.

The samples contain all information on the parameter space sampling (e.g. the parameters, log likelihoods, etc.).

The internal search results are converted from the native format used by the search to lists of values (e.g. parameter_lists, log_likelihood_list).

Parameters:

model – Maps input vectors of unit parameter values to physical values and model instances via priors.

config_dict_test_mode_from(config_dict)

Returns a configuration dictionary for test mode meaning that the sampler terminates as quickly as possible.

Entries which set the total number of samples of the sampler (e.g. maximum calls, maximum likelihood evaluations) are reduced to low values meaning it terminates nearly immediately.

Parameters:

config_dict (Dict) – The original configuration dictionary for this sampler which includes entries controlling how fast the sampler terminates.

Return type:

Dict

Returns:

• A configuration dictionary where settings which control the sampler’s number of samples are reduced so it

• terminates as quickly as possible.

property backend: HDFBackend

The Emcee hdf5 backend, which provides access to all samples, likelihoods, etc. of the non-linear search.

The sampler is described in the “Results” section at https://dynesty.readthedocs.io/en/latest/quickstart.html

Return type:

HDFBackend