from typing import Optional

import click

from clinica import option
from clinica.pipelines import cli_param
from clinica.pipelines.engine import clinica_pipeline

pipeline_name = "t1-freesurfer-longitudinal-correction"


@clinica_pipeline
@click.command(name=pipeline_name)
@cli_param.argument.caps_directory
@cli_param.option_group.common_pipelines_options
@cli_param.option.subjects_sessions_tsv
@cli_param.option.working_directory
@cli_param.option.overwrite_outputs
@cli_param.option.atlas_path
@option.global_option_group
@option.n_procs
@click.pass_context
def cli(
    ctx: click.Context,
    caps_directory: str,
    subjects_sessions_tsv: Optional[str] = None,
    working_directory: Optional[str] = None,
    n_procs: Optional[int] = None,
    overwrite_outputs: bool = False,
    atlas_path: Optional[str] = None,
) -> None:
    """Longitudinal pre-processing correction of T1w images with FreeSurfer.

    https://aramislab.paris.inria.fr/clinica/docs/public/latest/Pipelines/T1_FreeSurfer_Longitudinal/"
    """
    from networkx import Graph

    from clinica.pipelines.anatomical.freesurfer.atlas.cli import (
        cli as t1_freesurfer_atlas_cli,
    )
    from clinica.utils.ux import print_end_pipeline

    from .pipeline import T1FreeSurferLongitudinalCorrection

    pipeline = T1FreeSurferLongitudinalCorrection(
        caps_directory=caps_directory,
        tsv_file=subjects_sessions_tsv,
        base_dir=working_directory,
        name=pipeline_name,
        overwrite_caps=overwrite_outputs,
    )
    exec_pipeline = (
        pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})
        if n_procs
        else pipeline.run()
    )
    if isinstance(exec_pipeline, Graph):
        print_end_pipeline(
            pipeline_name, pipeline.base_dir, pipeline.base_dir_was_specified
        )
    if atlas_path is not None:
        ctx.invoke(
            t1_freesurfer_atlas_cli.cli,
            caps_directory=caps_directory,
            atlas_path=atlas_path,
            n_procs=n_procs,
        )


if __name__ == "__main__":
    cli()
