brain_pipe.cli.default.DefaultCLI¶

class DefaultCLI¶

Bases: CLI

Default CLI for brain_pipe.

Attributes

Methods

`__init__`()
`add_arguments_to_argparser`(argparser)	Add arguments to the argparser.
`get_argparser`([description])	Load the argparser.
`get_parser`(cli_info)	Find an appropriate parser based on the command line information.
`get_run_options`(parser, cli_info)	Extract a runner and Pipelines with their DataLoaders using the parser.
`parse_cli_arguments`([args])	Parse the command line arguments.
`parse_cli_arguments_for_parser`(parser, cli_info)	Parse the command line arguments.
`run`([args])	Run the command line interface.

add_arguments_to_argparser(argparser: ArgumentParser)¶

Add arguments to the argparser.

Parameters:: argparser (argparse.ArgumentParser) – Argparser to add arguments to.
Returns:: Argparser with added arguments.
Return type:: argparse.ArgumentParser

get_argparser(description='Preprocess brain imaging data')¶

Load the argparser.

get_parser(cli_info: Dict[str, Any])¶

Find an appropriate parser based on the command line information.

Parameters:: cli_info (Dict[str, Any]) – The parsed command line arguments.
Returns:: A parser that can be used to create Pipelines and runners.
Return type:: Parser

get_run_options(parser: Parser, cli_info: Dict[str, Any])¶

Extract a runner and Pipelines with their DataLoaders using the parser.

Parameters:

Returns:

A runner and a list of tuples containing a Pipeline and its DataLoader.

Return type:

Tuple[Runner, List[Tuple[Pipeline, DataLoader]]]

parse_cli_arguments(args=None)¶

Parse the command line arguments.

Parameters:: args (Any) – Arguments received from the command line. If None, the arguments should be parsed from sys.argv directly
Returns:: A dictionary containing the parsed arguments.
Return type:: Dict[str, Any]

parse_cli_arguments_for_parser(parser: Parser, cli_info: Dict[str, Any], args: Any | None = None) → Dict[str, Any]¶

Parse the command line arguments.

Parameters:

parser (Parser) – The parser to use to create the Pipelines and runner.
cli_info (Dict[str, Any]) – The parsed command line arguments.
args (Any) – Arguments received from the command line. If None, the arguments should be parsed from sys.argv directly

Returns:

A dictionary containing the parsed arguments.

Return type:

Dict[str, Any]

run(args: Any | None = None) → List[List[Dict[str, Any]]]¶

Run the command line interface.

Parameters:: args (Any) – Arguments received from the command line. If None, the arguments should be parsed from sys.argv directly
Returns:: A list of lists of data_dicts containing the results of the Pipelines.
Return type:: List[List[Dict[str, Any]]]