# SlicerPythonCLIExample

**Repository Path**: anxingle/SlicerPythonCLIExample

## Basic Information

- **Project Name**: SlicerPythonCLIExample
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: BSD-3-Clause
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2023-10-31
- **Last Updated**: 2023-10-31

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# SlicerPythonCLIExample
Example extension for 3D Slicer that demonstrates how to make a Python script available as a CLI module

Let's assume you have a [BlurImage.py](BlurImage/BlurImage.py) Python script that you can run from the command line as `python BlurImage.py input.nrrd 5.0 output.nrrd`. You can make this Python script available in Slicer using a nice auto-generated GUI just by adding a description of input and output parameters in a [Slicer Execution Model](https://www.slicer.org/wiki/Documentation/Nightly/Developers/SlicerExecutionModel) module descriptor XML file: [BlurImage.xml](BlurImage/BlurImage.xml).

Once `BlurImage` folder is added to additional module paths (or the extension package is installed), "Blur Image" module will show up in the module list (in Filtering / Denoising category) and can be used in Slicer as any other module.

![Auto-generated graphical user interface for Python script](BlurImageAutoGeneratedGUI.png)

The script can be executed from any other module, [the same way as other CLI modules](https://www.slicer.org/wiki/Documentation/Nightly/Developers/Python_scripting#Running_a_CLI_from_Python).

Example:

```python
import SampleData
inputImage = SampleData.downloadSample('MRHead')
outputImage = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLScalarVolumeNode', inputImage.GetName()+' blurred')

param = {}
param["inputVolume"] = inputImage.GetID()
param["outputVolume"] = outputImage.GetID()
param["sigma"] = 3.0
slicer.cli.runSync(slicer.modules.blurimage, parameters=param)
```