run_pipeline.py

#!/usr/bin/env python3
"""Run the full spike-sorting pipeline for one probe/shank."""

import argparse
import subprocess
import sys
from pathlib import Path

SCRIPT_DIR = Path(__file__).parent
PYTHON = sys.executable


def run(cmd: list[str]) -> None:
    subprocess.run(cmd, check=True, cwd=SCRIPT_DIR)


def main() -> None:
    parser = argparse.ArgumentParser()
    parser.add_argument("data_dir")
    parser.add_argument("probe", choices=["a", "b"])
    parser.add_argument("shank", choices=["0", "1", "2", "3"])
    args = parser.parse_args()

    run([PYTHON, "-u", str(SCRIPT_DIR / "pipeline" / "run_shank.py"), args.data_dir, args.probe, args.shank])
    run([PYTHON, str(SCRIPT_DIR / "pipeline" / "postproc.py"), args.data_dir, args.probe, args.shank])
    run([PYTHON, str(SCRIPT_DIR / "pipeline" / "extract_unitmatch_data.py"),
         "--data_dir", args.data_dir, "--probe", args.probe, "--shank", args.shank])


if __name__ == "__main__":
    main()