"""
Convert tractograms (TCK -> TRK).
"""
import os
import argparse

import nibabel as nib

from nibabel.streamlines import Field
from nibabel.orientations import aff2axcodes


def parse_args():
    DESCRIPTION = "Convert tractograms (TCK -> TRK)."
    parser = argparse.ArgumentParser(description=DESCRIPTION)
    parser.add_argument("anatomy",
                        help="reference anatomical image (.nii|.nii.gz.")
    parser.add_argument("tractograms", metavar="tractogram", nargs="+",
                        help="list of tractograms (.tck).")
    parser.add_argument("-f", "--force", action="store_true",
                        help="overwrite existing output files.")

    args = parser.parse_args()
    return args, parser


def main():
    args, parser = parse_args()

    try:
        nii = nib.load(args.anatomy)
    except Exception:
        parser.error("Expecting anatomical image as first agument.")

    for tractogram in args.tractograms:
        tractogram_format = nib.streamlines.detect_format(tractogram)
        if tractogram_format is not nib.streamlines.TckFile:
            print(f"Skipping non TCK file: '{tractogram}'")
            continue

        filename, _ = os.path.splitext(tractogram)
        output_filename = filename + '.trk'
        if os.path.isfile(output_filename) and not args.force:
            print(f"Skipping existing file: '{output_filename}'. Use -f to overwrite.")
            continue

        # Build header using infos from the anatomical image.
        header = {}
        header[Field.VOXEL_TO_RASMM] = nii.affine.copy()
        header[Field.VOXEL_SIZES] = nii.header.get_zooms()[:3]
        header[Field.DIMENSIONS] = nii.shape[:3]
        header[Field.VOXEL_ORDER] = "".join(aff2axcodes(nii.affine))

        tck = nib.streamlines.load(tractogram)
        nib.streamlines.save(tck.tractogram, output_filename, header=header)
