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ga_screening_protocol_amethyst

GA custom multi-algorithm protocol.

First runs a model inference on the GA model, then compute etdrs and the GA algorithm to compute the area affected by GA (as a whole and within the ETDRS subregions). Then CSV and PDF Reports get generated.

Classes​

GAScreeningProtocolAmethyst​

class GAScreeningProtocolAmethyst(    *,    algorithm: Sequence[Union[ModelInference, GATrialCalculationAlgorithmJade, TrialInclusionCriteriaMatchAlgorithmAmethyst, CSVReportGeneratorOphthalmologyAlgorithm, GATrialPDFGeneratorAlgorithmAmethyst]],    results_notification_email: Optional[bool] = False,    trial_name: Optional[str] = None,    rename_columns: Optional[Mapping[str, str]] = None,    **kwargs: Any,):

Protocol for running GA Algorithms sequentially.

Ancestors​

Variables​

  • algorithms : list - Returns the algorithms in the protocol.

Methods​

dump​

def dump(self) ‑> SerializedProtocol:

Inherited from:

BaseProtocolFactory.dump :

Returns the JSON-serializable representation of the protocol.

modeller​

def modeller(    self,    mailbox: _ModellerMailbox,    **kwargs: Any,) ‑> bitfount.federated.protocols.ophthalmology.ga_screening_protocol_amethyst._ModellerSide:

Returns the Modeller side of the protocol.

run​

def run(    self,    pod_identifiers: Collection[str],    session: Optional[BitfountSession] = None,    username: Optional[str] = None,    hub: Optional[BitfountHub] = None,    ms_config: Optional[MessageServiceConfig] = None,    message_service: Optional[_MessageService] = None,    pod_public_key_paths: Optional[Mapping[str, Path]] = None,    identity_verification_method: IdentityVerificationMethod = IdentityVerificationMethod.OIDC_DEVICE_CODE,    private_key_or_file: Optional[Union[RSAPrivateKey, Path]] = None,    idp_url: Optional[str] = None,    require_all_pods: bool = False,    run_on_new_data_only: bool = False,    model_out: Optional[Union[Path, str]] = None,    project_id: Optional[str] = None,    batched_execution: Optional[bool] = None,) ‑> Optional[Any]:

Inherited from:

BaseProtocolFactory.run :

Sets up a local Modeller instance and runs the protocol.

Arguments

  • pod_identifiers: The BitfountHub pod identifiers to run against.
  • session: Optional. Session to use for authenticated requests. Created if needed.
  • username: Username to run as. Defaults to logged in user.
  • hub: BitfountHub instance. Default: hub.bitfount.com.
  • ms_config: Message service config. Default: messaging.bitfount.com.
  • message_service: Message service instance, created from ms_config if not provided. Defaults to "messaging.bitfount.com".
  • pod_public_key_paths: Public keys of pods to be checked against.
  • identity_verification_method: The identity verification method to use.
  • private_key_or_file: Private key (to be removed).
  • idp_url: The IDP URL.
  • require_all_pods: If true raise PodResponseError if at least one pod identifier specified rejects or fails to respond to a task request.
  • run_on_new_data_only: Whether to run the task on new datapoints only. Defaults to False.
  • model_out: The path to save the model to.
  • project_id: The project ID to run the task under.
  • batched_execution: Whether to run the task in batched mode. Defaults to False.

Returns Results of the protocol.

Raises

  • PodResponseError: If require_all_pods is true and at least one pod identifier specified rejects or fails to respond to a task request.
  • ValueError: If attempting to train on multiple pods, and the DataStructure table name is given as a string.

worker​

def worker(self, mailbox: _WorkerMailbox, hub: BitfountHub, **kwargs: Any) ‑> _WorkerSide:

Returns worker side of the protocol.