sitk-cli 0.4.0

Wrap SimpleITK functions as command lines

Wrap SimpleITK functions as command lines

Overview

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

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))

Installation

pip install sitk-cli

Demo