main.py

"""
Run the complete workflow for the centerline computation from terminal
"""

import argparse
import json
from vessel_centerline.centerline_io import centerline_complete_workflow


def parse_args():
    parser = argparse.ArgumentParser(description="Compute centerlines with VTK")

    parser.add_argument(
        "--search-points",
        action="store_true",
        help="Get the coordinates of all the cap centers that are automatically found by the algorithm. You can use this coordinates to chose input and target points",
    )

    parser.add_argument(
        "--model-path",
        type=str,
        help="path to 3D vessel model, must be .stl or .vtp file",
    )
    parser.add_argument(
        "--source-point",
        default=None,
        type=json.loads,
        help="coordinates of centerline source point [x, y, z]",
    )
    parser.add_argument(
        "--target-points",
        default=None,
        nargs="*",
        type=json.loads,
        help="coordinates of centerline target points, list of lists: [[x1, y1, z1],[x2, y2, x2], ...]",
    )
    parser.add_argument(
        "--source-orientation",
        default=None,
        type=str,
        help="orientation of the source point on the model: 'up', 'down', 'left' or 'right'",
    )

    args = parser.parse_args()

    assert (
        (args.source_point and args.target_points)
        or args.source_orientation
        or args.search_points
    ), "you must specify source and target points coordinates or source orientation, otherwise you can search for points coordinates with find-points option"

    return args


if __name__ == "__main__":
    args = parse_args()
    centerline_complete_workflow(
        model_path=args.model_path,
        search_points=args.search_points,
        source_point=args.source_point,
        target_points=args.target_points,
        source_orientation=args.source_orientation,
        save_output_files=True,
    )