standalone dynamo to warp particle metadata conversion, to run `uv run dynamo2warp.py`

dynamo2warp.py

# /// script
# requires-python = ">=3.11"
# dependencies = [
#     "dynamotable",
#     "pandas",
#     "scipy",
#     "starfile",
#     "typer",
# ]
# [tool.uv]
# exclude-newer = "2025-01-01T00:00:00Z"
# ///

import re
from pathlib import Path

import dynamotable
import pandas as pd
import starfile
import typer
from scipy.spatial.transform import Rotation as R


def cli(
    input_table_file: Path = typer.Option(..., '--input', '--i', help='input table file'),
    table_map_file: Path = typer.Option(..., '--table-map', '--tm', help='table map file'),
    output_star_file: Path = typer.Option(..., '--output', '--o', help='output star file'),
):
    # read table file
    df = dynamotable.read(input_table_file, table_map_file=table_map_file)

    # extract relevant metadata
    positions = df[['x', 'y', 'z']].to_numpy()
    shifts = df[['dx', 'dy', 'dz']].to_numpy()
    dynamo_euler_angles = df[['tdrot', 'tilt', 'narot']].to_numpy()

    # convert dynamo euler angles into rotation matrices in which the
    # columns are the particle x/y/z vectors in the tomogram
    particle_rotation_matrices = R.from_euler(
        angles=dynamo_euler_angles, seq='zxz', degrees=True
    ).inv().as_matrix()

    # construct particle metadata for RELION
    positions += shifts
    relion_euler_angles = R.from_matrix(particle_rotation_matrices).inv().as_euler(
        seq='ZYZ', degrees=True
    )
    tomogram_files = df['tomo_file'].to_list()
    tomostar_files = [
        re.sub(pattern=r".mrc_\d+.\d+Apx.mrc", repl=".tomostar", string=tomogram_file)
        for tomogram_file
        in tomogram_files
    ]

    # write out RELION style star file compatible with Warp
    star_data = {
        'rlnCoordinateX': positions[:, 0],
        'rlnCoordinateY': positions[:, 1],
        'rlnCoordinateZ': positions[:, 2],
        'rlnAngleRot': relion_euler_angles[:, 0],
        'rlnAngleTilt': relion_euler_angles[:, 1],
        'rlnAnglePsi': relion_euler_angles[:, 2],
        'rlnMicrographName': tomostar_files,
    }
    starfile.write(pd.DataFrame(star_data), output_star_file)


if __name__ == "__main__":
    app = typer.Typer(add_completion=False)
    app.command(no_args_is_help=True)(cli)
    app()