dacapo.store.mongo_stats_store

Attributes

logger

Classes

MongoStatsStore

A MongoDB store for run statistics. Used to store and retrieve training

Module Contents

dacapo.store.mongo_stats_store.logger

class dacapo.store.mongo_stats_store.MongoStatsStore(db_host, db_name)

A MongoDB store for run statistics. Used to store and retrieve training statistics and validation scores.

db_host

The host of the MongoDB database.

Type:: str

db_name

The name of the MongoDB database.

Type:: str

client

The MongoDB client.

Type:: MongoClient

database

The MongoDB database.

Type:: Database

training_stats

The collection for training statistics.

Type:: Collection

validation_scores

The collection for validation scores.

Type:: Collection

store_training_stats(run_name, stats): Store the training stats of a given run.

retrieve_training_stats(run_name): Retrieve the training stats for a given run.

store_validation_iteration_scores(run_name, scores): Store the validation iteration scores of a given run.

retrieve_validation_iteration_scores(run_name): Retrieve the validation iteration scores for a given run.

delete_training_stats(run_name): Delete the training stats associated with a specific run.

Notes

The MongoStatsStore uses the ‘training_stats’ and ‘validation_scores’ collections to store the statistics.

db_host

db_name

client

database

store_training_stats(run_name: str, stats: dacapo.experiments.TrainingStats)

Store the training statistics for a specific run.

Parameters:

run_name (str) – The name of the run.
stats (TrainingStats) – The training statistics to be stored.

Raises:

ValueError – If the training statistics are already stored.

Examples

>>> store = MongoStatsStore('localhost', 'dacapo')
>>> run_name = 'run_0'
>>> stats = TrainingStats()
>>> store.store_training_stats(run_name, stats)

Notes

The training statistics are stored in the ‘training_stats’ collection.

retrieve_training_stats(run_name: str, subsample: bool = False) → dacapo.experiments.TrainingStats

Retrieve the training statistics for a given run.

Parameters:

run_name (str) – The name of the run.
subsample (bool, optional) – Whether to subsample the training statistics. Defaults to False.

Returns:

The training statistics for the specified run.

Return type:

TrainingStats

Raises:

ValueError – If the training statistics are not available.

Examples

>>> store = MongoStatsStore('localhost', 'dacapo')
>>> run_name = 'run_0'
>>> store.retrieve_training_stats(run_name)

Notes

The training statistics are retrieved from the ‘training_stats’ collection.

store_validation_iteration_scores(run_name: str, scores: dacapo.experiments.ValidationScores)

Stores the validation iteration scores for a given run.

Parameters:

run_name (str) – The name of the run.
scores (ValidationScores) – The validation scores to store.

Examples

>>> store = MongoStatsStore('localhost', 'dacapo')
>>> run_name = 'run_0'
>>> scores = ValidationScores()
>>> store.store_validation_iteration_scores(run_name, scores)

Notes

The validation iteration scores are stored in the ‘validation_scores’ collection.

retrieve_validation_iteration_scores(run_name: str, subsample: bool = False, validation_interval: int | None = None) → List[dacapo.experiments.ValidationIterationScores]

Retrieve the validation iteration scores for a given run.

Parameters:

run_name (str) – The name of the run.
subsample (bool, optional) – Whether to subsample the scores. Defaults to False.
validation_interval (int, optional) – The interval at which to retrieve the scores. Defaults to None.

Returns:

A list of validation iteration scores.

Return type:

List[ValidationIterationScores]

Raises:

ValueError – If the validation iteration scores are not available.

Examples

>>> store = MongoStatsStore('localhost', 'dacapo')
>>> run_name = 'run_0'
>>> store.retrieve_validation_iteration_scores(run_name)

Notes

The validation iteration scores are retrieved from the ‘validation_scores’ collection.

delete_validation_scores(run_name: str) → None

Deletes the validation scores for a given run.

Parameters:: run_name (str) – The name of the run for which validation scores should be deleted.
Raises:: ValueError – If the validation scores are not available.

Examples

>>> store = MongoStatsStore('localhost', 'dacapo')
>>> run_name = 'run_0'
>>> store.delete_validation_scores(run_name)

Notes

The validation scores are deleted from the ‘validation_scores’ collection.

delete_training_stats(run_name: str) → None

Deletes the training stats for a given run.

Parameters:: run_name (str) – The name of the run for which training stats should be deleted.
Raises:: ValueError – If the training statistics are not available.

Examples

>>> store = MongoStatsStore('localhost', 'dacapo')
>>> run_name = 'run_0'
>>> store.delete_training_stats(run_name)

Notes

The training statistics are deleted from the ‘training_stats’ collection.