sitk-cli 0.3.0

Wrap SimpleITK functions as command lines

Wrap SimpleITK functions as command lines

Create simple command line interface from functions that use SimpleITK images (and transforms) as arguments or return type.

Install from PyPI:

pip install sitk-cli

Example:

import SimpleITK as sitk
import typer

from sitk-cli import make_cli


def fill_holes_slice_by_slice(mask: sitk.Image) -> sitk.Image:
    mask = mask != 0
    output = sitk.Image(mask.GetSize(), mask.GetPixelID())
    output.CopyInformation(mask)
    for k in range(mask.GetSize()[2]):
        output[:, :, k] = sitk.BinaryFillhole(mask[:, :, k], fullyConnected=False)
    return output


if __name__ == "__main__":
    typer.run(make_cli(fill_holes_slice_by_slice))