Database¶

The default behaviour of PyAutoLens is for model-fitting results to be output to hard-disc in folders, which are straight forward to navigate and manually check the lens modeling results. For small samples of lenses this is sufficient, however many users have a need to perform many model fits to large lens datasets, making the manual inspection of results time consuming.

PyAutoLens’s database feature outputs all model-fitting results as a sqlite3 (https://docs.python.org/3/library/sqlite3.html) relational database, such that all results can be efficiently loaded into a Jupyter notebook or Python script for inspection, analysis and interpretation. This database supports advanced querying, so that specific model-fits (e.g., which fit a certain lens model or dataset) can be loaded.

To make it so that results are output to an .sqlite database we simply open a database session and pass this session to the non-linear search:

session = af.db.open_database("database.sqlite")

emcee = af.Emcee(
path_prefix=path.join("example", "database"),
session=session,  # This instructs the search to write to the .sqlite database.
)


When a model-fit is performed, a unique identifier is generated based on the model and non-linear search. However, if we were to fit many different lens datasets with the same model and non-linear search, they would all use the same unique identifier and not be distinguishable by the database.

We can overcome this by using the name of the dataset as the unique_tag passed to the search, which is used alongside the model and search to create the unique identifier:

session = af.db.open_database("database.sqlite")

dataset_name = "lens_dataset_0"

emcee = af.Emcee(
path_prefix=path.join("features", "database"),
unique_tag=dataset_name,  # This makes the unique identifier use the dataset name
session=session,  # This instructs the search to write to the .sqlite database.
)


Lets suppose that we have performed 100 model-fits to 100 strong lenses, and when we ran PyAutoLens we told it to write to the .sqlite database file. We can load these results in a Python script or Jupyter notebook using the Aggregator:

agg = Aggregator.from_database("path/to/output/database.sqlite")


We can now use the Aggregator to inspect the results of all model-fits. For example, we can load the Samples object of all 100 model-fits, which contains information on the best-fit model, posterior, Bayesian evidence, etc.

Below, we use the samples generator to create a list of the maximum log likelihood of every model-fit and print it:

for samples in agg.values("samples"):

print(max(samples.log_likelihood))


This object (and all objects loaded by the Aggregator) are returned as a generator (as opposed to a list, dictionary or other Python type). This is because generators do not store large arrays or classes in memory until they are used, ensuring that when we are manipulating large sets of results we do not run out of memory!

We can iterate over the samples to print the maximum log likelihood lens model of every fit:

for samps in agg.values("samples"):

instance = samps.max_log_likelihood_instance

print("Maximum Likelihood Model-fit \n")
print(instance)


The Aggregator contains tools for querying the database for certain results, for example to load subsets of model-fits. This can be done in many different ways, depending on what information you want.

Below, we query based on the model fitted. For example, we can load all results which fitted an EllIsothermal mass model (note that when we performed the model fit, we composed the lens model using a lens galaxy name lens and mass component named mass):

lens = agg.model.galaxies.lens
agg_query = agg.query(lens.mass == al.EllIsothermal)

samples_gen = agg_query.values("samples")


Queries using the results of model-fitting are also supported. Below, we query the database to find all fits where the inferred value of the einstein_radius for the EllIsothermal is above 1.0:

lens = agg.model.galaxies.lens


Advanced queries can be constructed using logic, for example we below we combine the two queries above to find all results which fitted an EllIsothermal AND (using the & symbol) inferred a value of sigma less than 3.0.

The OR logical clause is also supported via the symbol |.

agg_query = agg.query((lens.mass == al.EllIsothermal) & (lens.mass.einstein_radius > 1.0))


We can query using the unique_tag to load the model-fit to a specific dataset:

agg_query = agg.query(agg.unique_tag == "example_dataset_0")


An info dictionary can be passed into a model-fit, which contains information on the model-fit. The example below creates an info dictionary which is passed to the model-fit, which is then loaded via the database.

info = {"example_key": "example_value"}

emcee.fit(model=model, analysis=analysis, info=info)

agg = Aggregator.from_database("path/to/output/database.sqlite")

info_gen = agg.values("info")


Databases are an extremely powerful feature for users tasked with fitting extremely large datasets as well as fitting many different models, where the scale of the problem can make the management of the large quantity of results produced prohibitive. This is especially true on high performance computing facilities, which often have restrictions on the number of files that a user can store on the machine.

Furthermore, if you are using the SLaM pipelines, non-linear grid searches or sensitivity mapping features you’ll be aware that one can easily start generating thousands or millions of model-fits. There is no way to manage this large library of results other than the database!

A complete description of the database is given in the database folder on the autolens_workspace.