inr2tif.py

#!/usr/bin/env python
import argparse
from pathlib import Path

from timagetk.io import imread
from timagetk.io import imsave


def main(args):
    pin = Path(args.input)
    if pin.is_file():
        if pin.suffix != ".inr" and set(pin.suffixes) != set(".inr", ".gz"):
            raise ValueError("suffix should be one of .inr or .inr.gz")
        filenames = [pin]
    else:
        filenames = list(pin.glob("*.inr")) + list(pin.glob("*.inr.gz"))
    if args.output:
        pout = Path(args.output)
        pout.mkdir(parents=True, exist_ok=True)
    else:
        pout = pin.parent
    for filename in filenames:
        outfile = str(
            pout / str(filename).replace(".gz", "").replace(".inr", ".tif")
        )
        imsave(outfile, imread(str(filename)))


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Convert .inr or (.inr.gz) to .tif")
    parser.add_argument("input",
                        type=str,
                        help="input file or directory")
    parser.add_argument("-o", "--output",
                        type=str,
                        help="output directory")
    args = parser.parse_args()
    main(args)