https://github.com/dyollb/sitk-cli

Wrap SimpleITK functions as command lines
https://github.com/dyollb/sitk-cli

cli image-processing itk python simpleitk

Last synced: 2 months ago
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Wrap SimpleITK functions as command lines

• Host: GitHub
• URL: https://github.com/dyollb/sitk-cli
• Owner: dyollb
• License: mit
• Created: 2022-07-02T08:51:28.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-05-24T11:50:46.000Z (12 months ago)
• Last Synced: 2025-02-27T11:44:40.784Z (3 months ago)
• Topics: cli, image-processing, itk, python, simpleitk
• Language: Python
• Homepage:
• Size: 109 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Wrap SimpleITK functions as command lines

[![Build Actions Status](https://github.com/dyollb/segmantic/workflows/CI/badge.svg)](https://github.com/dyollb/sitk-cli/actions)

[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://https://opensource.org/licenses/MIT)

[![PyPI version](https://badge.fury.io/py/sitk-cli.svg)](https://badge.fury.io/py/sitk-cli)



## Overview

Create [Typer](https://github.com/tiangolo/typer) command line interface from functions that use [SimpleITK](https://github.com/SimpleITK/SimpleITK) images (and transforms) as arguments or return type.

```Python

import SimpleITK as sitk

import typer

from sitk_cli import register_command

app = typer.Typer()

@register_command(app)

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__":

    app()

```

To work, sitk-cli inspects the type annotations of the function and creates a wrapper function that loads images from file and passes these to the original function. Returned images (transforms) are written to a file by the wrapper function..

## Installation

```sh

pip install sitk-cli

```

## Demo

![Command lind demo](https://github.com/dyollb/sitk-cli/raw/main/docs/demo.gif)