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prepare

lacuna.cli.prepare

Prepare command implementation for the Lacuna CLI.

Handles lacuna prepare <analysis> — precomputation of the non-subject-specific data product a given analysis consumes. Targets are named after the analysis they prepare for (mirroring lacuna run). Currently the only target is afnm, which reduces a whole-brain functional connectome to the parcel-level connectivity matrix used by accelerated functional network mapping.

Commands: lacuna prepare afnm - Build the parcel-level connectivity matrix that 'lacuna run afnm' consumes via --matrix-path.

handle_prepare_command(args)

Dispatch the lacuna prepare subcommand by target.

Parameters:

Name Type Description Default
args Namespace

Parsed command-line arguments. args.prepare_target selects the precomputation target.

 required

Returns:

Type Description
int

Process exit code (0 on success).
Source code in src/lacuna/cli/prepare.py 
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def handle_prepare_command(args: argparse.Namespace) -> int:
    """Dispatch the ``lacuna prepare`` subcommand by target.

    Parameters
    ----------
    args : argparse.Namespace
        Parsed command-line arguments. ``args.prepare_target`` selects the
        precomputation target.

    Returns
    -------
    int
        Process exit code (0 on success).
    """
    target = getattr(args, "prepare_target", None)

    if target == "afnm":
        from lacuna.prepare.parcellate import run_parcellate_functional_cli

        return run_parcellate_functional_cli(args)

    print(
        "Error: 'lacuna prepare' requires a target. Try 'lacuna prepare afnm --help'.",
        file=sys.stderr,
    )
    return 1